Daily Papers

In this work, we introduce OmniGen2, a versatile and open-source generative model designed to provide a unified solution for diverse generation tasks, including text-to-image, image editing, and in-context generation. Unlike OmniGen v1, OmniGen2 features two distinct decoding pathways for text and image modalities, utilizing unshared parameters and a decoupled image tokenizer. This design enables OmniGen2 to build upon existing multimodal understanding models without the need to re-adapt VAE inputs, thereby preserving the original text generation capabilities. To facilitate the training of OmniGen2, we developed comprehensive data construction pipelines, encompassing image editing and in-context generation data. Additionally, we introduce a reflection mechanism tailored for image generation tasks and curate a dedicated reflection dataset based on OmniGen2. Despite its relatively modest parameter size, OmniGen2 achieves competitive results on multiple task benchmarks, including text-to-image and image editing. To further evaluate in-context generation, also referred to as subject-driven tasks, we introduce a new benchmark named OmniContext. OmniGen2 achieves state-of-the-art performance among open-source models in terms of consistency. We will release our models, training code, datasets, and data construction pipeline to support future research in this field. Project Page: https://vectorspacelab.github.io/OmniGen2; GitHub Link: https://github.com/VectorSpaceLab/OmniGen2

A critical component of a successful language generation pipeline is the decoding algorithm. However, the general principles that should guide the choice of decoding algorithm remain unclear. Previous works only compare decoding algorithms in narrow scenarios and their findings do not generalize across tasks. To better structure the discussion, we introduce a taxonomy that groups decoding strategies based on their implicit assumptions about how well the model's likelihood is aligned with the task-specific notion of utility. We argue that this taxonomy allows a broader view of the decoding problem and can lead to generalizable statements because it is grounded on the interplay between the decoding algorithms and the likelihood-utility misalignment. Specifically, by analyzing the correlation between the likelihood and the utility of predictions across a diverse set of tasks, we provide the first empirical evidence supporting the proposed taxonomy, and a set of principles to structure reasoning when choosing a decoding algorithm. Crucially, our analysis is the first one to relate likelihood-based decoding strategies with strategies that rely on external information such as value-guided methods and prompting, and covers the most diverse set of tasks up-to-date.

In enhancing the reasoning capabilities of large language models (LLMs), prior research primarily focuses on specific prompting techniques such as few-shot or zero-shot chain-of-thought (CoT) prompting. These methods, while effective, often involve manually intensive prompt engineering. Our study takes a novel approach by asking: Can LLMs reason effectively without prompting? Our findings reveal that, intriguingly, CoT reasoning paths can be elicited from pre-trained LLMs by simply altering the decoding process. Rather than conventional greedy decoding, we investigate the top-k alternative tokens, uncovering that CoT paths are frequently inherent in these sequences. This approach not only bypasses the confounders of prompting but also allows us to assess the LLMs' intrinsic reasoning abilities. Moreover, we observe that the presence of a CoT in the decoding path correlates with a higher confidence in the model's decoded answer. This confidence metric effectively differentiates between CoT and non-CoT paths. Extensive empirical studies on various reasoning benchmarks show that the proposed CoT-decoding substantially outperforms the standard greedy decoding.

Contrastive Language-Image Pre-training (CLIP) has accomplished extraordinary success for semantic understanding but inherently struggles to perceive geometric structure. Existing methods attempt to bridge this gap by querying CLIP with textual prompts, a process that is often indirect and inefficient. This paper introduces a fundamentally different approach using a dual-pathway decoder. We present SPACE-CLIP, an architecture that unlocks and interprets latent geometric knowledge directly from a frozen CLIP vision encoder, completely bypassing the text encoder and its associated textual prompts. A semantic pathway interprets high-level features, dynamically conditioned on global context using feature-wise linear modulation (FiLM). In addition, a structural pathway extracts fine-grained spatial details from early layers. These complementary streams are hierarchically fused, enabling a robust synthesis of semantic context and precise geometry. Extensive experiments on the KITTI benchmark show that SPACE-CLIP dramatically outperforms previous CLIP-based methods. Our ablation studies validate that the synergistic fusion of our dual pathways is critical to this success. SPACE-CLIP offers a new, efficient, and architecturally elegant blueprint for repurposing large-scale vision models. The proposed method is not just a standalone depth estimator, but a readily integrable spatial perception module for the next generation of embodied AI systems, such as vision-language-action (VLA) models. Our model is available at https://github.com/taewan2002/space-clip

Genetic pathways usually encode molecular mechanisms that can inform targeted interventions. It is often challenging for existing machine learning approaches to jointly model genetic pathways (higher-order features) and variants (atomic features), and present to clinicians interpretable models. In order to build more accurate and better interpretable machine learning models for genetic medicine, we introduce Pathway Augmented Nonnegative Tensor factorization for HighER-order feature learning (PANTHER). PANTHER selects informative genetic pathways that directly encode molecular mechanisms. We apply genetically motivated constrained tensor factorization to group pathways in a way that reflects molecular mechanism interactions. We then train a softmax classifier for disease types using the identified pathway groups. We evaluated PANTHER against multiple state-of-the-art constrained tensor/matrix factorization models, as well as group guided and Bayesian hierarchical models. PANTHER outperforms all state-of-the-art comparison models significantly (p<0.05). Our experiments on large scale Next Generation Sequencing (NGS) and whole-genome genotyping datasets also demonstrated wide applicability of PANTHER. We performed feature analysis in predicting disease types, which suggested insights and benefits of the identified pathway groups.

Inference-time optimization scales computation to derive deliberate reasoning steps for effective performance. While previous search-based strategies address the short-sightedness of auto-regressive generation, the vast search space leads to excessive exploration and insufficient exploitation. To strike an efficient balance to derive the optimal step, we frame the decoding strategy as foresight sampling, leveraging simulated future steps to obtain globally optimal step estimation. Built on it, we propose a novel decoding strategy, named phi-Decoding. To provide a precise and expressive estimation of step value, phi-Decoding approximates two distributions via foresight and clustering. Sampling from the joint distribution, the optimal steps can be selected for exploitation. To support adaptive computation allocation, we propose in-width and in-depth pruning strategies, featuring a light-weight solution to achieve inference efficiency. Extensive experiments across seven benchmarks show phi-Decoding outperforms strong baselines in both performance and efficiency. Additional analysis demonstrates its generalization across various LLMs and scalability across a wide range of computing budgets. The code will be released at https://github.com/xufangzhi/phi-Decoding, and the open-source PyPI package is coming soon.

Pathology diagnosis based on EEG signals and decoding brain activity holds immense importance in understanding neurological disorders. With the advancement of artificial intelligence methods and machine learning techniques, the potential for accurate data-driven diagnoses and effective treatments has grown significantly. However, applying machine learning algorithms to real-world datasets presents diverse challenges at multiple levels. The scarcity of labelled data, especially in low regime scenarios with limited availability of real patient cohorts due to high costs of recruitment, underscores the vital deployment of scaling and transfer learning techniques. In this study, we explore a real-world pathology classification task to highlight the effectiveness of data and model scaling and cross-dataset knowledge transfer. As such, we observe varying performance improvements through data scaling, indicating the need for careful evaluation and labelling. Additionally, we identify the challenges of possible negative transfer and emphasize the significance of some key components to overcome distribution shifts and potential spurious correlations and achieve positive transfer. We see improvement in the performance of the target model on the target (NMT) datasets by using the knowledge from the source dataset (TUAB) when a low amount of labelled data was available. Our findings indicate a small and generic model (e.g. ShallowNet) performs well on a single dataset, however, a larger model (e.g. TCN) performs better on transfer and learning from a larger and diverse dataset.

Interpreting the inner function of neural networks is crucial for the trustworthy development and deployment of these black-box models. Prior interpretability methods focus on correlation-based measures to attribute model decisions to individual examples. However, these measures are susceptible to noise and spurious correlations encoded in the model during the training phase (e.g., biased inputs, model overfitting, or misspecification). Moreover, this process has proven to result in noisy and unstable attributions that prevent any transparent understanding of the model's behavior. In this paper, we develop a robust interventional-based method grounded by causal analysis to capture cause-effect mechanisms in pre-trained neural networks and their relation to the prediction. Our novel approach relies on path interventions to infer the causal mechanisms within hidden layers and isolate relevant and necessary information (to model prediction), avoiding noisy ones. The result is task-specific causal explanatory graphs that can audit model behavior and express the actual causes underlying its performance. We apply our method to vision models trained on classification tasks. On image classification tasks, we provide extensive quantitative experiments to show that our approach can capture more stable and faithful explanations than standard attribution-based methods. Furthermore, the underlying causal graphs reveal the neural interactions in the model, making it a valuable tool in other applications (e.g., model repair).

We propose to improve transformers of a specific modality with irrelevant data from other modalities, e.g., improve an ImageNet model with audio or point cloud datasets. We would like to highlight that the data samples of the target modality are irrelevant to the other modalities, which distinguishes our method from other works utilizing paired (e.g., CLIP) or interleaved data of different modalities. We propose a methodology named Multimodal Pathway - given a target modality and a transformer designed for it, we use an auxiliary transformer trained with data of another modality and construct pathways to connect components of the two models so that data of the target modality can be processed by both models. In this way, we utilize the universal sequence-to-sequence modeling abilities of transformers obtained from two modalities. As a concrete implementation, we use a modality-specific tokenizer and task-specific head as usual but utilize the transformer blocks of the auxiliary model via a proposed method named Cross-Modal Re-parameterization, which exploits the auxiliary weights without any inference costs. On the image, point cloud, video, and audio recognition tasks, we observe significant and consistent performance improvements with irrelevant data from other modalities. The code and models are available at https://github.com/AILab-CVC/M2PT.

To mitigate the high inference latency stemming from autoregressive decoding in Large Language Models (LLMs), Speculative Decoding has emerged as a novel decoding paradigm for LLM inference. In each decoding step, this method first efficiently drafts several future tokens and then verifies them in parallel. Unlike autoregressive decoding, Speculative Decoding facilitates the simultaneous decoding of multiple tokens per step, thereby accelerating inference. This paper presents a comprehensive overview and analysis of this promising decoding paradigm. We begin by providing a formal definition and formulation of Speculative Decoding. Then, we organize in-depth discussions on its key facets, including current leading techniques, the challenges faced, and potential future directions in this field. We aim for this work to serve as a catalyst for further research on Speculative Decoding, ultimately contributing to more efficient LLM inference.

In recent years, large-scale transformer decoders such as the GPT-x family of models have become increasingly popular. Studies examining the behavior of these models tend to focus only on the output of the language modeling head and avoid analysis of the internal states of the transformer decoder. In this study, we present a collection of methods to analyze the hidden states of GPT-2 and use the model's navigation of garden path sentences as a case study. To enable this, we compile the largest currently available dataset of garden path sentences. We show that Manhattan distances and cosine similarities provide more reliable insights compared to established surprisal methods that analyze next-token probabilities computed by a language modeling head. Using these methods, we find that negating tokens have minimal impacts on the model's representations for unambiguous forms of sentences with ambiguity solely over what the object of a verb is, but have a more substantial impact of representations for unambiguous sentences whose ambiguity would stem from the voice of a verb. Further, we find that analyzing the decoder model's hidden states reveals periods of ambiguity that might conclude in a garden path effect but happen not to, whereas surprisal analyses routinely miss this detail.

The end-to-end nature of neural machine translation (NMT) removes many ways of manually guiding the translation process that were available in older paradigms. Recent work, however, has introduced a new capability: lexically constrained or guided decoding, a modification to beam search that forces the inclusion of pre-specified words and phrases in the output. However, while theoretically sound, existing approaches have computational complexities that are either linear (Hokamp and Liu, 2017) or exponential (Anderson et al., 2017) in the number of constraints. We present a algorithm for lexically constrained decoding with a complexity of O(1) in the number of constraints. We demonstrate the algorithms remarkable ability to properly place these constraints, and use it to explore the shaky relationship between model and BLEU scores. Our implementation is available as part of Sockeye.

Transformers use the dense self-attention mechanism which gives a lot of flexibility for long-range connectivity. Over multiple layers of a deep transformer, the number of possible connectivity patterns increases exponentially. However, very few of these contribute to the performance of the network, and even fewer are essential. We hypothesize that there are sparsely connected sub-networks within a transformer, called information pathways which can be trained independently. However, the dynamic (i.e., input-dependent) nature of these pathways makes it difficult to prune dense self-attention during training. But the overall distribution of these pathways is often predictable. We take advantage of this fact to propose Stochastically Subsampled self-Attention (SSA) - a general-purpose training strategy for transformers that can reduce both the memory and computational cost of self-attention by 4 to 8 times during training while also serving as a regularization method - improving generalization over dense training. We show that an ensemble of sub-models can be formed from the subsampled pathways within a network, which can achieve better performance than its densely attended counterpart. We perform experiments on a variety of NLP, computer vision and graph learning tasks in both generative and discriminative settings to provide empirical evidence for our claims and show the effectiveness of the proposed method.

In recent years, many interpretability methods have been proposed to help interpret the internal states of Transformer-models, at different levels of precision and complexity. Here, to analyze encoder-decoder Transformers, we propose a simple, new method: DecoderLens. Inspired by the LogitLens (for decoder-only Transformers), this method involves allowing the decoder to cross-attend representations of intermediate encoder layers instead of using the final encoder output, as is normally done in encoder-decoder models. The method thus maps previously uninterpretable vector representations to human-interpretable sequences of words or symbols. We report results from the DecoderLens applied to models trained on question answering, logical reasoning, speech recognition and machine translation. The DecoderLens reveals several specific subtasks that are solved at low or intermediate layers, shedding new light on the information flow inside the encoder component of this important class of models.

Neural decoding, the process of understanding how brain activity corresponds to different stimuli, has been a primary objective in cognitive sciences. Over the past three decades, advancements in functional Magnetic Resonance Imaging and machine learning have greatly improved our ability to map visual stimuli to brain activity, especially in the visual cortex. Concurrently, research has expanded into decoding more complex processes like language and memory across the whole brain, utilizing techniques to handle greater variability and improve signal accuracy. We argue that "seeing" involves more than just mapping visual stimuli onto the visual cortex; it engages the entire brain, as various emotions and cognitive states can emerge from observing different scenes. In this paper, we develop algorithms to enhance our understanding of visual processes by incorporating whole-brain activation maps while individuals are exposed to visual stimuli. We utilize large-scale fMRI encoders and Image generative models pre-trained on large public datasets, which are then fine-tuned through Image-fMRI contrastive learning. Our models hence can decode visual experience across the entire cerebral cortex, surpassing the traditional confines of the visual cortex. We first compare our method with state-of-the-art approaches to decoding visual processing and show improved predictive semantic accuracy by 43%. A network ablation analysis suggests that beyond the visual cortex, the default mode network contributes most to decoding stimuli, in line with the proposed role of this network in sense-making and semantic processing. Additionally, we implemented zero-shot imagination decoding on an extra validation dataset, achieving a p-value of 0.0206 for mapping the reconstructed images and ground-truth text stimuli, which substantiates the model's capability to capture semantic meanings across various scenarios.

Information flows by routes inside the network via mechanisms implemented in the model. These routes can be represented as graphs where nodes correspond to token representations and edges to operations inside the network. We automatically build these graphs in a top-down manner, for each prediction leaving only the most important nodes and edges. In contrast to the existing workflows relying on activation patching, we do this through attribution: this allows us to efficiently uncover existing circuits with just a single forward pass. Additionally, the applicability of our method is far beyond patching: we do not need a human to carefully design prediction templates, and we can extract information flow routes for any prediction (not just the ones among the allowed templates). As a result, we can talk about model behavior in general, for specific types of predictions, or different domains. We experiment with Llama 2 and show that the role of some attention heads is overall important, e.g. previous token heads and subword merging heads. Next, we find similarities in Llama 2 behavior when handling tokens of the same part of speech. Finally, we show that some model components can be specialized on domains such as coding or multilingual texts.

Diffusion Language Models (DLMs) have recently emerged as a strong alternative to autoregressive language models (LMs). DLMs offer comparable accuracy with faster inference speed via parallel decoding. However, standard DLM decoding strategies relying on high-confidence tokens encounter an inherent information-theoretic bottleneck that restricts decoding progress and ultimately slows generation. We demonstrate both theoretically and empirically that prioritizing high-confidence tokens is inherently inefficient. High-probability tokens carry negligible information and strictly relying on them limits the effective progress made in each decoding round. We prove that the number of decoding rounds must grow linearly with the sample's total information (negative log-likelihood) and inversely with the per-round information budget, establishing a bits-to-rounds principle. We also propose Explore-Then-Exploit (ETE), a training-free decoding strategy that maximizes information throughput and decoding efficiency. ETE combines cross-block decoding with targeted exploration of high-uncertainty tokens to reshape the conditional distribution and trigger cascades of confident predictions. Experiments verify our theoretical bounds and demonstrate that ETE consistently reduces the required number of decoding rounds compared to confidence-only baselines without compromising generation quality.

Decoding methods play an indispensable role in converting language models from next-token predictors into practical task solvers. Prior research on decoding methods, primarily focusing on task-specific models, may not extend to the current era of general-purpose large language models (LLMs). Moreover, the recent influx of decoding strategies has further complicated this landscape. This paper provides a comprehensive and multifaceted analysis of various decoding methods within the context of LLMs, evaluating their performance, robustness to hyperparameter changes, and decoding speeds across a wide range of tasks, models, and deployment environments. Our findings reveal that decoding method performance is notably task-dependent and influenced by factors such as alignment, model size, and quantization. Intriguingly, sensitivity analysis exposes that certain methods achieve superior performance at the cost of extensive hyperparameter tuning, highlighting the trade-off between attaining optimal results and the practicality of implementation in varying contexts.

Every day, the human brain processes an immense volume of visual information, relying on intricate neural mechanisms to perceive and interpret these stimuli. Recent breakthroughs in functional magnetic resonance imaging (fMRI) have enabled scientists to extract visual information from human brain activity patterns. In this study, we present an innovative method for decoding brain activity into meaningful images and captions, with a specific focus on brain captioning due to its enhanced flexibility as compared to brain decoding into images. Our approach takes advantage of cutting-edge image captioning models and incorporates a unique image reconstruction pipeline that utilizes latent diffusion models and depth estimation. We utilized the Natural Scenes Dataset, a comprehensive fMRI dataset from eight subjects who viewed images from the COCO dataset. We employed the Generative Image-to-text Transformer (GIT) as our backbone for captioning and propose a new image reconstruction pipeline based on latent diffusion models. The method involves training regularized linear regression models between brain activity and extracted features. Additionally, we incorporated depth maps from the ControlNet model to further guide the reconstruction process. We evaluate our methods using quantitative metrics for both generated captions and images. Our brain captioning approach outperforms existing methods, while our image reconstruction pipeline generates plausible images with improved spatial relationships. In conclusion, we demonstrate significant progress in brain decoding, showcasing the enormous potential of integrating vision and language to better understand human cognition. Our approach provides a flexible platform for future research, with potential applications in various fields, including neural art, style transfer, and portable devices.

Drug discovery is a complex and time-intensive process that requires identifying and validating new therapeutic candidates. Computational approaches using large-scale biomedical knowledge graphs (KGs) offer a promising solution to accelerate this process. However, extracting meaningful insights from large-scale KGs remains challenging due to the complexity of graph traversal. Existing subgraph-based methods are tailored to graph neural networks (GNNs), making them incompatible with other models, such as large language models (LLMs). We introduce K-Paths, a retrieval framework that extracts structured, diverse, and biologically meaningful paths from KGs. Integrating these paths enables LLMs and GNNs to effectively predict unobserved drug-drug and drug-disease interactions. Unlike traditional path-ranking approaches, K-Paths retrieves and transforms paths into a structured format that LLMs can directly process, facilitating explainable reasoning. K-Paths employs a diversity-aware adaptation of Yen's algorithm to retrieve the K shortest loopless paths between entities in an interaction query, prioritizing biologically relevant and diverse relationships. Our experiments on benchmark datasets show that K-Paths improves the zero-shot performance of Llama 8.1B's F1-score by 12.45 points on drug repurposing and 13.42 points on interaction severity prediction. We also show that Llama 70B achieves F1-score gains of 6.18 and 8.46 points, respectively. K-Paths also improves the supervised training efficiency of EmerGNN, a state-of-the-art GNN, by reducing KG size by 90% while maintaining strong predictive performance. Beyond its scalability and efficiency, K-Paths uniquely bridges the gap between KGs and LLMs, providing explainable rationales for predicted interactions. These capabilities show that K-Paths is a valuable tool for efficient data-driven drug discovery.

Diffusion Language Models (DLMs) have recently achieved significant success due to their any-order generation capabilities. However, existing inference methods typically rely on local, immediate-step metrics such as confidence or entropy which inherently lack a more reliable perspective. This limitation frequently leads to inconsistent sampling trajectories and suboptimal generation quality. To address this, we propose Coherent Contextual Decoding (CCD), a novel inference framework built upon two core innovations. First, CCD employs a trajectory rectification mechanism that leverages historical context to enhance sequence coherence, enabling the early rejection of suboptimal paths. We demonstrate that this mechanism is theoretically equivalent to modeling the consistency of historical steps via the conditional mutual information between context and token predictions. Building on this theoretical insight, we further address the inefficiency of conventional uniform decoding budgets. Instead of rigid allocations based on diffusion steps, we introduce an adaptive sampling strategy that dynamically adjusts the unmasking budget for each step according to our consistency metric. Consequently, our method significantly improves the quality of generation trajectories while accelerating the sampling process. Empirically, our method achieves a simultaneous enhancement in both inference speed and performance across diverse benchmarks on Dream and LLaDA, delivering up to 3.48x speedup alongside 3.91% performance improvement.

Large Language Models (LLMs) are prone to hallucination, the generation of plausible yet factually incorrect statements. This work investigates the intrinsic, architectural origins of this failure mode through three primary contributions.First, to enable the reliable tracing of internal semantic failures, we propose Distributional Semantics Tracing (DST), a unified framework that integrates established interpretability techniques to produce a causal map of a model's reasoning, treating meaning as a function of context (distributional semantics). Second, we pinpoint the model's layer at which a hallucination becomes inevitable, identifying a specific commitment layer where a model's internal representations irreversibly diverge from factuality. Third, we identify the underlying mechanism for these failures. We observe a conflict between distinct computational pathways, which we interpret using the lens of dual-process theory: a fast, heuristic associative pathway (akin to System 1) and a slow, deliberate contextual pathway (akin to System 2), leading to predictable failure modes such as Reasoning Shortcut Hijacks. Our framework's ability to quantify the coherence of the contextual pathway reveals a strong negative correlation (rho = -0.863) with hallucination rates, implying that these failures are predictable consequences of internal semantic weakness. The result is a mechanistic account of how, when, and why hallucinations occur within the Transformer architecture.

In this paper, we present UNet++, a new, more powerful architecture for medical image segmentation. Our architecture is essentially a deeply-supervised encoder-decoder network where the encoder and decoder sub-networks are connected through a series of nested, dense skip pathways. The re-designed skip pathways aim at reducing the semantic gap between the feature maps of the encoder and decoder sub-networks. We argue that the optimizer would deal with an easier learning task when the feature maps from the decoder and encoder networks are semantically similar. We have evaluated UNet++ in comparison with U-Net and wide U-Net architectures across multiple medical image segmentation tasks: nodule segmentation in the low-dose CT scans of chest, nuclei segmentation in the microscopy images, liver segmentation in abdominal CT scans, and polyp segmentation in colonoscopy videos. Our experiments demonstrate that UNet++ with deep supervision achieves an average IoU gain of 3.9 and 3.4 points over U-Net and wide U-Net, respectively.

Mechanistic interpretability seeks to understand the neural mechanisms that enable specific behaviors in Large Language Models (LLMs) by leveraging causality-based methods. While these approaches have identified neural circuits that copy spans of text, capture factual knowledge, and more, they remain unusable for multimodal models since adapting these tools to the vision-language domain requires considerable architectural changes. In this work, we adapt a unimodal causal tracing tool to BLIP to enable the study of the neural mechanisms underlying image-conditioned text generation. We demonstrate our approach on a visual question answering dataset, highlighting the causal relevance of later layer representations for all tokens. Furthermore, we release our BLIP causal tracing tool as open source to enable further experimentation in vision-language mechanistic interpretability by the community. Our code is available at https://github.com/vedantpalit/Towards-Vision-Language-Mechanistic-Interpretability.

Multivariate time series anomalies often manifest as shifts in cross-channel dependencies rather than simple amplitude excursions. In autonomous driving, for instance, a steering command might be internally consistent but decouple from the resulting lateral acceleration. Residual-based detectors can miss such anomalies when flexible sequence models still reconstruct signals plausibly despite altered coordination. We introduce AxonAD, an unsupervised detector that treats multi-head attention query evolution as a short horizon predictable process. A gradient-updated reconstruction pathway is coupled with a history-only predictor that forecasts future query vectors from past context. This is trained via a masked predictor-target objective against an exponential moving average (EMA) target encoder. At inference, reconstruction error is combined with a tail-aggregated query mismatch score, which measures cosine deviation between predicted and target queries on recent timesteps. This dual approach provides sensitivity to structural dependency shifts while retaining amplitude-level detection. On proprietary in-vehicle telemetry with interval annotations and on the TSB-AD multi-variate suite (17 datasets, 180 series) with threshold-free and range-aware metrics, AxonAD improves ranking quality and temporal localization over strong baselines. Ablations confirm that query prediction and combined scoring are the primary drivers of the observed gains. Code is available at the URL https://github.com/iis-esslingen/AxonAD.

A central goal for mechanistic interpretability has been to identify the right units of analysis in large language models (LLMs) that causally explain their outputs. While early work focused on individual neurons, evidence that neurons often encode multiple concepts has motivated a shift toward analyzing directions in activation space. A key question is how to find directions that capture interpretable features in an unsupervised manner. Current methods rely on dictionary learning with sparse autoencoders (SAEs), commonly trained over residual stream activations to learn directions from scratch. However, SAEs often struggle in causal evaluations and lack intrinsic interpretability, as their learning is not explicitly tied to the computations of the model. Here, we tackle these limitations by directly decomposing MLP activations with semi-nonnegative matrix factorization (SNMF), such that the learned features are (a) sparse linear combinations of co-activated neurons, and (b) mapped to their activating inputs, making them directly interpretable. Experiments on Llama 3.1, Gemma 2 and GPT-2 show that SNMF derived features outperform SAEs and a strong supervised baseline (difference-in-means) on causal steering, while aligning with human-interpretable concepts. Further analysis reveals that specific neuron combinations are reused across semantically-related features, exposing a hierarchical structure in the MLP's activation space. Together, these results position SNMF as a simple and effective tool for identifying interpretable features and dissecting concept representations in LLMs.

We present the Pathways Autoregressive Text-to-Image (Parti) model, which generates high-fidelity photorealistic images and supports content-rich synthesis involving complex compositions and world knowledge. Parti treats text-to-image generation as a sequence-to-sequence modeling problem, akin to machine translation, with sequences of image tokens as the target outputs rather than text tokens in another language. This strategy can naturally tap into the rich body of prior work on large language models, which have seen continued advances in capabilities and performance through scaling data and model sizes. Our approach is simple: First, Parti uses a Transformer-based image tokenizer, ViT-VQGAN, to encode images as sequences of discrete tokens. Second, we achieve consistent quality improvements by scaling the encoder-decoder Transformer model up to 20B parameters, with a new state-of-the-art zero-shot FID score of 7.23 and finetuned FID score of 3.22 on MS-COCO. Our detailed analysis on Localized Narratives as well as PartiPrompts (P2), a new holistic benchmark of over 1600 English prompts, demonstrate the effectiveness of Parti across a wide variety of categories and difficulty aspects. We also explore and highlight limitations of our models in order to define and exemplify key areas of focus for further improvements. See https://parti.research.google/ for high-resolution images.

Autoregressive decoding limits the efficiency of transformers for Machine Translation (MT). The community proposed specific network architectures and learning-based methods to solve this issue, which are expensive and require changes to the MT model, trading inference speed at the cost of the translation quality. In this paper, we propose to address the problem from the point of view of decoding algorithms, as a less explored but rather compelling direction. We propose to reframe the standard greedy autoregressive decoding of MT with a parallel formulation leveraging Jacobi and Gauss-Seidel fixed-point iteration methods for fast inference. This formulation allows to speed up existing models without training or modifications while retaining translation quality. We present three parallel decoding algorithms and test them on different languages and models showing how the parallelization introduces a speedup up to 38% w.r.t. the standard autoregressive decoding and nearly 2x when scaling the method on parallel resources. Finally, we introduce a decoding dependency graph visualizer (DDGviz) that let us see how the model has learned the conditional dependence between tokens and inspect the decoding procedure.

High-quality chain-of-thought has demonstrated strong potential for unlocking the reasoning capabilities of large language models. However, current paradigms typically treat the reasoning process as an indivisible sequence, lacking an intrinsic mechanism to quantify step-wise information gain. This granularity gap manifests in two limitations: inference inefficiency from redundant exploration without explicit guidance, and optimization difficulty due to sparse outcome supervision or costly external verifiers. In this work, we propose CoT-Flow, a framework that reconceptualizes discrete reasoning steps as a continuous probabilistic flow, quantifying the contribution of each step toward the ground-truth answer. Built on this formulation, CoT-Flow enables two complementary methodologies: flow-guided decoding, which employs a greedy flow-based decoding strategy to extract information-efficient reasoning paths, and flow-based reinforcement learning, which constructs a verifier-free dense reward function. Experiments on challenging benchmarks demonstrate that CoT-Flow achieves a superior balance between inference efficiency and reasoning performance.

Despite the progress in machine translation quality estimation and evaluation in the last years, decoding in neural machine translation (NMT) is mostly oblivious to this and centers around finding the most probable translation according to the model (MAP decoding), approximated with beam search. In this paper, we bring together these two lines of research and propose quality-aware decoding for NMT, by leveraging recent breakthroughs in reference-free and reference-based MT evaluation through various inference methods like N-best reranking and minimum Bayes risk decoding. We perform an extensive comparison of various possible candidate generation and ranking methods across four datasets and two model classes and find that quality-aware decoding consistently outperforms MAP-based decoding according both to state-of-the-art automatic metrics (COMET and BLEURT) and to human assessments. Our code is available at https://github.com/deep-spin/qaware-decode.

Speculative decoding is a technique that uses multiple language models to accelerate infer- ence. Previous works have used an experi- mental approach to optimize the throughput of the inference pipeline, which involves LLM training and can be costly. This study of spec- ulative decoding proposes a theory that ana- lytically connects the key hyperparameters of pre-trained LLMs to the throughput efficiency of a downstream SD-based inference system. The theory allows the prediction of throughput- optimal hyperparameters for the components of an inference system before their pre-training.

Next token prediction paradigm has been prevailing for autoregressive models in the era of LLMs. The current default sampling choice for popular LLMs is temperature scaling together with nucleus sampling to balance diversity and coherence. Nevertheless, such approach leads to inferior performance in various NLP tasks when the model is not certain about testing questions. To this end, we propose a brand new training-free decoding strategy, dubbed as Cautious Next Token Prediction (CNTP). In the decoding process, if the model has comparatively high prediction entropy at a certain step, we sample multiple trials starting from the step independently and stop when encountering any punctuation. Then we select the trial with the lowest perplexity score viewed as the most probable and reliable trial path given the model's capacity. The trial number is negatively correlated with the prediction confidence, i.e., the less confident the model is, the more trials it should sample. This is consistent with human beings' behaviour: when feeling uncertain or unconfident, one tends to think more creatively, exploring multiple thinking paths, to cautiously select the path one feels most confident about. Extensive experiments on both LLMs and MLLMs show that our proposed CNTP approach outperforms existing standard decoding strategies consistently by a clear margin. Moreover, the integration of CNTP with self consistency can further improve over vanilla self consistency. We believe our proposed CNTP has the potential to become one of the default choices for LLM decoding. Code is available at https://github.com/wyzjack/CNTP.

Hierarchical classification offers an approach to incorporate the concept of mistake severity by leveraging a structured, labeled hierarchy. However, decoding in such settings frequently relies on heuristic decision rules, which may not align with task-specific evaluation metrics. In this work, we propose a framework for the optimal decoding of an output probability distribution with respect to a target metric. We derive optimal decision rules for increasingly complex prediction settings, providing universal algorithms when candidates are limited to the set of nodes. In the most general case of predicting a subset of nodes, we focus on rules dedicated to the hierarchical hF_{beta} scores, tailored to hierarchical settings. To demonstrate the practical utility of our approach, we conduct extensive empirical evaluations, showcasing the superiority of our proposed optimal strategies, particularly in underdetermined scenarios. These results highlight the potential of our methods to enhance the performance and reliability of hierarchical classifiers in real-world applications. The code is available at https://github.com/RomanPlaud/hierarchical_decision_rules

Diffusion Language Models (DLMs) offer order-agnostic generation that can explore many possible decoding trajectories. However, current decoding methods commit to a single trajectory, limiting exploration in trajectory space. We introduce Order-Token Search to explore this space through jointly searching over generation order and token values. Its core is a likelihood estimator that scores denoising actions, enabling stable pruning and efficient exploration of diverse trajectories. Across mathematical reasoning and coding benchmarks, Order-Token Search consistently outperforms baselines on GSM8K, MATH500, Countdown, and HumanEval (3.1%, 3.8%, 7.9%, and 6.8% absolute over backbone), matching or surpassing diffu-GRPO post-trained d1-LLaDA. Our work establishes joint search as a key component for advancing decoding in DLMs.

Recent studies have revealed a number of pathologies of neural machine translation (NMT) systems. Hypotheses explaining these mostly suggest there is something fundamentally wrong with NMT as a model or its training algorithm, maximum likelihood estimation (MLE). Most of this evidence was gathered using maximum a posteriori (MAP) decoding, a decision rule aimed at identifying the highest-scoring translation, i.e. the mode. We argue that the evidence corroborates the inadequacy of MAP decoding more than casts doubt on the model and its training algorithm. In this work, we show that translation distributions do reproduce various statistics of the data well, but that beam search strays from such statistics. We show that some of the known pathologies and biases of NMT are due to MAP decoding and not to NMT's statistical assumptions nor MLE. In particular, we show that the most likely translations under the model accumulate so little probability mass that the mode can be considered essentially arbitrary. We therefore advocate for the use of decision rules that take into account the translation distribution holistically. We show that an approximation to minimum Bayes risk decoding gives competitive results confirming that NMT models do capture important aspects of translation well in expectation.

In neural decoding research, one of the most intriguing topics is the reconstruction of perceived natural images based on fMRI signals. Previous studies have succeeded in re-creating different aspects of the visuals, such as low-level properties (shape, texture, layout) or high-level features (category of objects, descriptive semantics of scenes) but have typically failed to reconstruct these properties together for complex scene images. Generative AI has recently made a leap forward with latent diffusion models capable of generating high-complexity images. Here, we investigate how to take advantage of this innovative technology for brain decoding. We present a two-stage scene reconstruction framework called ``Brain-Diffuser''. In the first stage, starting from fMRI signals, we reconstruct images that capture low-level properties and overall layout using a VDVAE (Very Deep Variational Autoencoder) model. In the second stage, we use the image-to-image framework of a latent diffusion model (Versatile Diffusion) conditioned on predicted multimodal (text and visual) features, to generate final reconstructed images. On the publicly available Natural Scenes Dataset benchmark, our method outperforms previous models both qualitatively and quantitatively. When applied to synthetic fMRI patterns generated from individual ROI (region-of-interest) masks, our trained model creates compelling ``ROI-optimal'' scenes consistent with neuroscientific knowledge. Thus, the proposed methodology can have an impact on both applied (e.g. brain-computer interface) and fundamental neuroscience.

Image degradation from blur, noise, compression, and poor illumination severely undermines multimodal understanding in real-world settings. Unified multimodal models that combine understanding and generation within a single architecture are a natural fit for this challenge, as their generative pathway can model the fine-grained visual structure that degradation destroys. Yet these models fail to leverage their own generative capacity on degraded inputs. We trace this disconnect to two compounding factors: existing training regimes never ask the model to invoke generation during reasoning, and the standard decode-reencode pathway does not support effective joint optimization. We present CLEAR, a framework that connects the two capabilities through three progressive steps: (1) supervised fine-tuning on a degradation-aware dataset to establish the generate-then-answer reasoning pattern; (2) a Latent Representation Bridge that replaces the decode-reencode detour with a direct, optimizable connection between generation and reasoning; (3) Interleaved GRPO, a reinforcement learning method that jointly optimizes text reasoning and visual generation under answer-correctness rewards. We construct MMD-Bench, covering three degradation severity levels across six standard multimodal benchmarks. Experiments show that CLEAR substantially improves robustness on degraded inputs while preserving clean-image performance. Our analysis further reveals that removing pixel-level reconstruction supervision leads to intermediate visual states with higher perceptual quality, suggesting that task-driven optimization and visual quality are naturally aligned.

Large language model (LLM) decoding involves generating a sequence of tokens based on a given context, where each token is predicted one at a time using the model's learned probabilities. The typical autoregressive decoding method requires a separate forward pass through the model for each token generated, which is computationally inefficient and poses challenges for deploying LLMs in latency-sensitive scenarios. The main limitations of current decoding methods stem from their inefficiencies and resource demands. Existing approaches either necessitate fine-tuning smaller models, which is resource-intensive, or rely on fixed retrieval schemes to construct drafts for the next tokens, which lack adaptability and fail to generalize across different models and contexts. To address these issues, we introduce a novel methodology called ADED, which accelerates LLM decoding without requiring fine-tuning. Our approach involves an adaptive draft-verification process that evolves over time to improve efficiency. We utilize a tri-gram matrix-based LLM representation to dynamically approximate the output distribution of the LLM, allowing the model to adjust to changing token probabilities during the decoding process. Additionally, we implement a draft construction mechanism that effectively balances exploration and exploitation, ensuring that the drafts generated are both diverse and close to the true output distribution of the LLM. The importance of this design lies in its ability to optimize the draft distribution adaptively, leading to faster and more accurate decoding. Through extensive experiments on various benchmark datasets and LLM architectures, we demonstrate that ADED significantly accelerates the decoding process while maintaining high accuracy, making it suitable for deployment in a wide range of practical applications.

This paper localizes the policy routing mechanism in alignment-trained language models. An intermediate-layer attention gate reads detected content and triggers deeper amplifier heads that boost the signal toward refusal. In smaller models the gate and amplifier are single heads; at larger scale they become bands of heads across adjacent layers. The gate contributes under 1% of output DLA, but interchange testing (p<0.001) and knockout cascade confirm it is causally necessary. Interchange screening at n>=120 detects the same motif in twelve models from six labs (2B to 72B), though specific heads differ by lab. Per-head ablation weakens up to 58x at 72B and misses gates that interchange identifies; interchange is the only reliable audit at scale. Modulating the detection-layer signal continuously controls policy from hard refusal through evasion to factual answering. On safety prompts the same intervention turns refusal into harmful guidance, showing the safety-trained capability is gated by routing rather than removed. Thresholds vary by topic and by input language, and the circuit relocates across generations within a family while behavioral benchmarks register no change. Routing is early-commitment: the gate commits at its own layer before deeper layers finish processing the input. Under an in-context substitution cipher, gate interchange necessity collapses 70 to 99% across three models and the model switches to puzzle-solving. Injecting the plaintext gate activation into the cipher forward pass restores 48% of refusals in Phi-4-mini, localizing the bypass to the routing interface. A second method, cipher contrast analysis, uses plain/cipher DLA differences to map the full cipher-sensitive routing circuit in O(3n) forward passes. Any encoding that defeats detection-layer pattern matching bypasses the policy regardless of whether deeper layers reconstruct the content.

Diffusion language models (DLMs) generate text through iterative denoising, but inference requires full-sequence attention at every iteration, resulting in substantial redundant computation on masked tokens. Block-wise diffusion can reduce this cost, yet it typically relies on retraining and constrained update orders, limiting its direct applicability to pretrained DLMs. Our token-level analysis reveals pronounced structural locality in DLM inference. Decoding is driven by a small set of prefix-localized active tokens; the influence of distant undecoded context diminishes rapidly, and decoded tokens exhibit stage-wise temporal stability, enabling reuse of intermediate representations except for a brief post-decode transient. Motivated by these observations, we propose \placeholderThe source code is available at https://github.com/vhicrgit/Window-Diffusion., a window-based token pruning and caching method for inference. We maintain a local computation window that slides rightward as denoising progresses, and partition undecoded tokens into: (i) active tokens that are computed online, (ii) buffer tokens whose KV states are cached and periodically refreshed, and (iii) far-field tokens that are pruned outside the window. Computation is restricted to active and buffer tokens within the window, while far-field tokens are omitted at each stage. Experiments on LLaDA and Dream show that, under matched compute budgets, our method achieves up to 99times inference speedup while largely preserving generation performance.

Brain decoding, a pivotal field in neuroscience, aims to reconstruct stimuli from acquired brain signals, primarily utilizing functional magnetic resonance imaging (fMRI). Currently, brain decoding is confined to a per-subject-per-model paradigm, limiting its applicability to the same individual for whom the decoding model is trained. This constraint stems from three key challenges: 1) the inherent variability in input dimensions across subjects due to differences in brain size; 2) the unique intrinsic neural patterns, influencing how different individuals perceive and process sensory information; 3) limited data availability for new subjects in real-world scenarios hampers the performance of decoding models. In this paper, we present a novel approach, MindBridge, that achieves cross-subject brain decoding by employing only one model. Our proposed framework establishes a generic paradigm capable of addressing these challenges by introducing biological-inspired aggregation function and novel cyclic fMRI reconstruction mechanism for subject-invariant representation learning. Notably, by cycle reconstruction of fMRI, MindBridge can enable novel fMRI synthesis, which also can serve as pseudo data augmentation. Within the framework, we also devise a novel reset-tuning method for adapting a pretrained model to a new subject. Experimental results demonstrate MindBridge's ability to reconstruct images for multiple subjects, which is competitive with dedicated subject-specific models. Furthermore, with limited data for a new subject, we achieve a high level of decoding accuracy, surpassing that of subject-specific models. This advancement in cross-subject brain decoding suggests promising directions for wider applications in neuroscience and indicates potential for more efficient utilization of limited fMRI data in real-world scenarios. Project page: https://littlepure2333.github.io/MindBridge

Efficient inference in large language models (LLMs) has become a critical focus as their scale and complexity grow. Traditional autoregressive decoding, while effective, suffers from computational inefficiencies due to its sequential token generation process. Speculative decoding addresses this bottleneck by introducing a two-stage framework: drafting and verification. A smaller, efficient model generates a preliminary draft, which is then refined by a larger, more sophisticated model. This paper provides a comprehensive survey of speculative decoding methods, categorizing them into draft-centric and model-centric approaches. We discuss key ideas associated with each method, highlighting their potential for scaling LLM inference. This survey aims to guide future research in optimizing speculative decoding and its integration into real-world LLM applications.

Masked Diffusion Models (MDMs) offer flexible, non-autoregressive generation, but this freedom introduces a challenge: final output quality is highly sensitive to the decoding order. We are the first to formalize this issue, attributing the variability in output quality to the cumulative predictive uncertainty along a generative path. To quantify this uncertainty, we introduce Denoising Entropy, a computable metric that serves as an internal signal for evaluating generative process. Leveraging this metric, we propose two algorithms designed to optimize the decoding path: a post-hoc selection method and a real-time guidance strategy. Experiments demonstrate that our entropy-guided methods significantly improve generation quality, consistently boosting accuracy on challenging reasoning, planning, and code benchmarks. Our work establishes Denoising Entropy as a principled tool for understanding and controlling generation, effectively turning the uncertainty in MDMs from a liability into a key advantage for discovering high-quality solutions.

Modern Large Language Models achieve impressive reasoning capabilities with long Chain of Thoughts, but they incur substantial computational cost during inference, and this motivates techniques to improve the performance-cost ratio. Among these techniques, Speculative Decoding accelerates inference by employing a fast but inaccurate draft model to autoregressively propose tokens, which are then verified in parallel by a more capable target model. However, due to unnecessary rejections caused by token mismatches in semantically equivalent steps, traditional token-level Speculative Decoding struggles in reasoning tasks. Although recent works have shifted to step-level semantic verification, which improve efficiency by accepting or rejecting entire reasoning steps, existing step-level methods still regenerate many rejected steps with little improvement, wasting valuable target compute. To address this challenge, we propose Arbitrage, a novel step-level speculative generation framework that routes generation dynamically based on the relative advantage between draft and target models. Instead of applying a fixed acceptance threshold, Arbitrage uses a lightweight router trained to predict when the target model is likely to produce a meaningfully better step. This routing approximates an ideal Arbitrage Oracle that always chooses the higher-quality step, achieving near-optimal efficiency-accuracy trade-offs. Across multiple mathematical reasoning benchmarks, Arbitrage consistently surpasses prior step-level Speculative Decoding baselines, reducing inference latency by up to sim2times at matched accuracy.

Given a prefix (context), open-ended generation aims to decode texts that are coherent, which do not abruptly drift from previous topics, and informative, which do not suffer from undesired repetitions. In this paper, we propose Look-back, an improved decoding algorithm that leverages the Kullback-Leibler divergence to track the distribution distance between current and historical decoding steps. Thus Look-back can automatically predict potential repetitive phrase and topic drift, and remove tokens that may cause the failure modes, restricting the next token probability distribution within a plausible distance to the history. We perform decoding experiments on document continuation and story generation, and demonstrate that Look-back is able to generate more fluent and coherent text, outperforming other strong decoding methods significantly in both automatic and human evaluations.

Generative recommendation via autoregressive models has unified retrieval and ranking into a single conditional generation framework. However, fine-tuning these models with Reinforcement Learning (RL) often suffers from a fundamental probability-reward mismatch. Conventional likelihood-dominated decoding (e.g., beam search) exhibits a myopic bias toward locally probable prefixes, which causes two critical failures: (1) insufficient exploration, where high-reward items in low-probability branches are prematurely pruned and rarely sampled, and (2) advantage compression, where trajectories sharing high-probability prefixes receive highly correlated rewards with low within-group variance, yielding a weak comparative signal for RL. To address these challenges, we propose V-STAR, a Value-guided Sampling and Tree-structured Advantage Reinforcement framework. V-STAR forms a self-evolving loop via two synergistic components. First, a Value-Guided Efficient Decoding (VED) is developed to identify decisive nodes and selectively deepen high-potential prefixes. This improves exploration efficiency without exhaustive tree search. Second, we propose Sibling-GRPO, which exploits the induced tree topology to compute sibling-relative advantages and concentrates learning signals on decisive branching decisions. Extensive experiments on both offline and online datasets demonstrate that V-STAR outperforms state-of-the-art baselines, delivering superior accuracy and candidate-set diversity under strict latency constraints.

Hallucination mitigation remains a persistent challenge for large language models (LLMs), even as model scales grow. Existing approaches often rely on external knowledge sources, such as structured databases or knowledge graphs, accessed through prompting or retrieval. However, prompt-based grounding is fragile and domain-sensitive, while symbolic knowledge integration incurs heavy retrieval and formatting costs. Motivated by knowledge graphs, we introduce Graph-Retrieved Adaptive Decoding (GRAD), a decoding-time method that grounds generation in corpus-derived evidence without retraining. GRAD constructs a sparse token transition graph by accumulating next-token logits across a small retrieved corpus in a single forward pass. During decoding, graph-retrieved logits are max-normalized and adaptively fused with model logits to favor high-evidence continuations while preserving fluency. Across three models and a range of question-answering benchmarks spanning intrinsic, extrinsic hallucination, and factuality tasks, GRAD consistently surpasses baselines, achieving up to 9.7% higher intrinsic accuracy, 8.6% lower hallucination rates, and 6.9% greater correctness compared to greedy decoding, while attaining the highest truth--informativeness product score among all methods. GRAD offers a lightweight, plug-and-play alternative to contrastive decoding and knowledge graph augmentation, demonstrating that statistical evidence from corpus-level token transitions can effectively steer generation toward more truthful and verifiable outputs.

Decoding language from brain activity is a long-awaited goal in both healthcare and neuroscience. Major milestones have recently been reached thanks to intracranial devices: subject-specific pipelines trained on invasive brain responses to basic language tasks now start to efficiently decode interpretable features (e.g. letters, words, spectrograms). However, scaling this approach to natural speech and non-invasive brain recordings remains a major challenge. Here, we propose a single end-to-end architecture trained with contrastive learning across a large cohort of individuals to predict self-supervised representations of natural speech. We evaluate our model on four public datasets, encompassing 169 volunteers recorded with magneto- or electro-encephalography (M/EEG), while they listened to natural speech. The results show that our model can identify, from 3s of MEG signals, the corresponding speech segment with up to 72.5% top-10 accuracy out of 1,594 distinct segments (and 44% top-1 accuracy), and up to 19.1% out of 2,604 segments for EEG recordings -- hence allowing the decoding of phrases absent from the training set. Model comparison and ablation analyses show that these performances directly benefit from our original design choices, namely the use of (i) a contrastive objective, (ii) pretrained representations of speech and (iii) a common convolutional architecture simultaneously trained across several participants. Together, these results delineate a promising path to decode natural language processing in real time from non-invasive recordings of brain activity.

Chain-of-Thought (CoT) reasoning has significantly advanced the problem-solving capabilities of Large Language Models (LLMs), yet conventional CoT often exhibits internal determinism during decoding, limiting exploration of plausible alternatives. Recent methods attempt to address this by generating soft abstract tokens to enable reasoning in a continuous semantic space. However, we find that such approaches remain constrained by the greedy nature of autoregressive decoding, which fundamentally isolates the model from alternative reasoning possibilities. In this work, we propose Multi-Path Perception Policy Optimization (M3PO), a novel reinforcement learning framework that explicitly injects collective insights into the reasoning process. M3PO leverages parallel policy rollouts as naturally diverse reasoning sources and integrates cross-path interactions into policy updates through a lightweight collaborative mechanism. This design allows each trajectory to refine its reasoning with peer feedback, thereby cultivating more reliable multi-step reasoning patterns. Empirical results show that M3PO achieves state-of-the-art performance on both knowledge- and reasoning-intensive benchmarks. Models trained with M3PO maintain interpretability and inference efficiency, underscoring the promise of multi-path collaborative learning for robust reasoning.

The recent development of chain-of-thought (CoT) decoding has enabled large language models (LLMs) to generate explicit logical reasoning paths for complex problem-solving. However, research indicates that these paths are not always deliberate and optimal. The tree-of-thought (ToT) method employs tree-searching to extensively explore the reasoning space and find better reasoning paths that CoT decoding might overlook. This deliberation, however, comes at the cost of significantly increased inference complexity. In this work, we demonstrate that fine-tuning LLMs leveraging the search tree constructed by ToT allows CoT to achieve similar or better performance, thereby avoiding the substantial inference burden. This is achieved through Chain of Preference Optimization (CPO), where LLMs are fine-tuned to align each step of the CoT reasoning paths with those of ToT using the inherent preference information in the tree-search process. Extensive experimental results show that CPO significantly improves LLM performance in solving a variety of complex problems, including question answering, fact verification, and arithmetic reasoning, demonstrating its effectiveness. Our code is available at https://github.com/sail-sg/CPO.

We present Connection-Aware Motif Sequencing (CamS), a graph-to-sequence representation that enables decoder-only Transformers to learn molecular graphs via standard next-token prediction (NTP). For molecular property prediction, SMILES-based NTP scales well but lacks explicit topology, whereas graph-native masked modeling captures connectivity but risks disrupting the pivotal chemical details (e.g., activity cliffs). CamS bridges this gap by serializing molecular graphs into structure-rich causal sequences. CamS first mines data-driven connection-aware motifs. It then serializes motifs via scaffold-rooted breadth-first search (BFS) to establish a stable core-to-periphery order. Crucially, CamS enables hierarchical modeling by concatenating sequences from fine to coarse motif scales, allowing the model to condition global scaffolds on dense, uncorrupted local structural evidence. We instantiate CamS-LLaMA by pre-training a vanilla LLaMA backbone on CamS sequences. It achieves state-of-the-art performance on MoleculeNet and the activity-cliff benchmark MoleculeACE, outperforming both SMILES-based language models and strong graph baselines. Interpretability analysis confirms that our multi-scale causal serialization effectively drives attention toward cliff-determining differences.

Conditional neural text generation models generate high-quality outputs, but often concentrate around a mode when what we really want is a diverse set of options. We present a search algorithm to construct lattices encoding a massive number of generation options. First, we restructure decoding as a best-first search, which explores the space differently than beam search and improves efficiency by avoiding pruning paths. Second, we revisit the idea of hypothesis recombination: we can identify pairs of similar generation candidates during search and merge them as an approximation. On both summarization and machine translation, we show that our algorithm encodes thousands of diverse options that remain grammatical and high-quality into one lattice. This algorithm provides a foundation for building downstream generation applications on top of massive-scale diverse outputs.

Methods for knowledge editing and unlearning in large language models seek to edit or remove undesirable knowledge or capabilities without compromising general language modeling performance. This work investigates how mechanistic interpretability -- which, in part, aims to identify model components (circuits) associated to specific interpretable mechanisms that make up a model capability -- can improve the precision and effectiveness of editing and unlearning. We find a stark difference in unlearning and edit robustness when training components localized by different methods. We highlight an important distinction between methods that localize components based primarily on preserving outputs, and those finding high level mechanisms with predictable intermediate states. In particular, localizing edits/unlearning to components associated with the lookup-table mechanism for factual recall 1) leads to more robust edits/unlearning across different input/output formats, and 2) resists attempts to relearn the unwanted information, while also reducing unintended side effects compared to baselines, on both a sports facts dataset and the CounterFact dataset across multiple models. We also find that certain localized edits disrupt the latent knowledge in the model more than any other baselines, making unlearning more robust to various attacks.

Large language models (LLMs) are increasingly adept at following instructions containing task descriptions to solve complex problems, such as mathematical reasoning and automatic evaluation (LLM-as-a-Judge). However, as prompts grow more complex, models often struggle to adhere to all instructions. This difficulty is especially common when instructive prompts intertwine reasoning directives -- specifying what the model should solve -- with rigid formatting requirements that dictate how the solution must be presented. The entanglement creates competing goals for the model, suggesting that more explicit separation of these two aspects could lead to improved performance. To this front, we introduce Deco-G, a decoding framework that explicitly decouples format adherence from task solving. Deco-G handles format compliance with a separate tractable probabilistic model (TPM), while prompts LLMs with only task instructions. At each decoding step, Deco-G combines next token probabilities from the LLM with the TPM calculated format compliance likelihood to form the output probability. To make this approach both practical and scalable for modern instruction-tuned LLMs, we introduce three key innovations: instruction-aware distillation, a flexible trie-building algorithm, and HMM state pruning for computational efficiency. We demonstrate the effectiveness of Deco-G across a wide range of tasks with diverse format requirements, including mathematical reasoning, LLM-as-a-judge, and event argument extraction. Overall, our approach yields 1.0% to 6.0% relative gain over regular prompting practice with guaranteed format compliance.

We propose a simple auto-encoder framework for molecule generation. The molecular graph is first encoded into a continuous latent representation z, which is then decoded back to a molecule. The encoding process is easy, but the decoding process remains challenging. In this work, we introduce a simple two-step decoding process. In a first step, a fully connected neural network uses the latent vector z to produce a molecular formula, for example CO_2 (one carbon and two oxygen atoms). In a second step, a graph convolutional neural network uses the same latent vector z to place bonds between the atoms that were produced in the first step (for example a double bond will be placed between the carbon and each of the oxygens). This two-step process, in which a bag of atoms is first generated, and then assembled, provides a simple framework that allows us to develop an efficient molecule auto-encoder. Numerical experiments on basic tasks such as novelty, uniqueness, validity and optimized chemical property for the 250k ZINC molecules demonstrate the performances of the proposed system. Particularly, we achieve the highest reconstruction rate of 90.5\%, improving the previous rate of 76.7\%. We also report the best property improvement results when optimization is constrained by the molecular distance between the original and generated molecules.

We introduce directional routing, a lightweight mechanism that gives each transformer attention head learned suppression directions controlled by a shared router, at 3.9% parameter cost. We train a 433M-parameter model alongside an identical baseline in a single run, then trace the resulting circuits through mechanistic interpretability. Routing becomes the model's dominant computational pathway. Disabling it collapses factual recall to near-zero probability across all 8 test prompts and drops induction accuracy from 93.4% to 0.0%. Knocking out individual attention heads has negligible effect: the primary mover head's removal actually increases target probability, and induction heads retain 98.6% accuracy without their strongest member. The coordination mechanism is irreplaceable; the components it coordinates are not. The model also self-organizes, without explicit pressure, into two regimes: domain-adaptive routing in early layers and fixed syntactic pruning in late layers, where the least-varying layer is the most critical (+42.6 PPL when disabled). Routing reduces perplexity 31-56% relative to the baseline, though downstream multiple-choice benchmarks do not yet reflect these gains.

Large language model (LLM) routers improve the efficiency of multi-model systems by directing each query to the most appropriate model while leveraging the diverse strengths of heterogeneous LLMs. Most existing approaches frame routing as a classification problem based solely on the input query. While this reduces overhead by avoiding inference across all models, it overlooks valuable information that could be gleaned from potential outputs and fails to capture implicit intent or contextual nuances that often emerge only during response generation. These limitations can result in suboptimal routing decisions, particularly for complex or ambiguous queries that require deeper semantic understanding. To address this challenge, we propose Lookahead, a routing framework that "foresees" potential model outputs by predicting their latent representations and uses these predictions to guide model selection, thus enabling more informed routing without full inference. Within this framework, we implement two approaches based on causal and masked language models. Empirical evaluations across seven public benchmarks - spanning instruction following, mathematical reasoning, and code generation - show that Lookahead consistently outperforms existing routing baselines, achieving an average performance gain of 7.7% over the state-of-the-art. Our code is available at https://github.com/huangcb01/lookahead-routing.

Recent alignment studies commonly remove introductory boilerplate phrases from supervised fine-tuning (SFT) datasets. This work challenges that assumption. We hypothesize that safety- and reasoning-oriented prefix sentences serve as lightweight alignment signals that can guide model decoding toward safer and more coherent responses. To examine this, we fine-tune three R1 series models across three core model capabilities: reasoning (mathematics, coding), safety, and factuality, systematically varying prefix inclusion from 0% to 100%. Results show that prefix-conditioned SFT improves both safety and reasoning performance, yielding up to +6% higher Safe@1 accuracy on adversarial benchmarks (WildJailbreak, StrongReject) and +7% improvement on GSM8K reasoning. However, factuality and coding tasks show marginal or negative effects, indicating that prefix-induced narrowing of the search space benefits structured reasoning. Token-level loss analysis further reveals that prefix tokens such as "revised" and "logically" incur higher gradient magnitudes, acting as alignment anchors that stabilize reasoning trajectories. Our findings suggest that prefix conditioning offers a scalable and interpretable mechanism for improving reasoning safety, serving as an implicit form of alignment that complements traditional reward-based methods.

Hallucinations in large language models are a widespread problem, yet the mechanisms behind whether models will hallucinate are poorly understood, limiting our ability to solve this problem. Using sparse autoencoders as an interpretability tool, we discover that a key part of these mechanisms is entity recognition, where the model detects if an entity is one it can recall facts about. Sparse autoencoders uncover meaningful directions in the representation space, these detect whether the model recognizes an entity, e.g. detecting it doesn't know about an athlete or a movie. This suggests that models can have self-knowledge: internal representations about their own capabilities. These directions are causally relevant: capable of steering the model to refuse to answer questions about known entities, or to hallucinate attributes of unknown entities when it would otherwise refuse. We demonstrate that despite the sparse autoencoders being trained on the base model, these directions have a causal effect on the chat model's refusal behavior, suggesting that chat finetuning has repurposed this existing mechanism. Furthermore, we provide an initial exploration into the mechanistic role of these directions in the model, finding that they disrupt the attention of downstream heads that typically move entity attributes to the final token.

Large Language Models (LLMs) are increasingly required to generate text that is both factually accurate and diverse across various open-ended applications. However, current stochastic decoding methods struggle to balance such objectives. We introduce Dynamic Focus Decoding (DFD), a novel plug-and-play stochastic approach that resolves this trade-off without requiring additional data, knowledge, or models. DFD adaptively adjusts the decoding focus based on distributional differences across layers, leveraging the modular and hierarchical nature of factual knowledge within LLMs. This dynamic adjustment improves factuality in knowledge-intensive decoding steps and promotes diversity in less knowledge-reliant steps. DFD can be easily integrated with existing decoding methods, enhancing both factuality and diversity with minimal computational overhead. Extensive experiments across seven datasets demonstrate that DFD significantly improves performance, providing a scalable and efficient solution for open-ended text generation.

Recent research in decoding methods for Natural Language Generation (NLG) tasks has shown that MAP decoding is not optimal, because model probabilities do not always align with human preferences. Stronger decoding methods, including Quality Estimation (QE) reranking and Minimum Bayes' Risk (MBR) decoding, have since been proposed to mitigate the model-perplexity-vs-quality mismatch. While these decoding methods achieve state-of-the-art performance, they are prohibitively expensive to compute. In this work, we propose MBR finetuning and QE finetuning which distill the quality gains from these decoding methods at training time, while using an efficient decoding algorithm at inference time. Using the canonical NLG task of Neural Machine Translation (NMT), we show that even with self-training, these finetuning methods significantly outperform the base model. Moreover, when using an external LLM as a teacher model, these finetuning methods outperform finetuning on human-generated references. These findings suggest new ways to leverage monolingual data to achieve improvements in model quality that are on par with, or even exceed, improvements from human-curated data, while maintaining maximum efficiency during decoding.

Scientific Large Language Models (Sci-LLMs) have emerged as a promising frontier for accelerating biological discovery. However, these models face a fundamental challenge when processing raw biomolecular sequences: the tokenization dilemma. Whether treating sequences as a specialized language, risking the loss of functional motif information, or as a separate modality, introducing formidable alignment challenges, current strategies fundamentally limit their reasoning capacity. We challenge this sequence-centric paradigm by positing that a more effective strategy is to provide Sci-LLMs with high-level structured context derived from established bioinformatics tools, thereby bypassing the need to interpret low-level noisy sequence data directly. Through a systematic comparison of leading Sci-LLMs on biological reasoning tasks, we tested three input modes: sequence-only, context-only, and a combination of both. Our findings are striking: the context-only approach consistently and substantially outperforms all other modes. Even more revealing, the inclusion of the raw sequence alongside its high-level context consistently degrades performance, indicating that raw sequences act as informational noise, even for models with specialized tokenization schemes. These results suggest that the primary strength of existing Sci-LLMs lies not in their nascent ability to interpret biomolecular syntax from scratch, but in their profound capacity for reasoning over structured, human-readable knowledge. Therefore, we argue for reframing Sci-LLMs not as sequence decoders, but as powerful reasoning engines over expert knowledge. This work lays the foundation for a new class of hybrid scientific AI agents, repositioning the developmental focus from direct sequence interpretation towards high-level knowledge synthesis. The code is available at https://github.com/opendatalab-raiser/CoKE.

Single-shot neural decoders commit to answers without iterative refinement, while chain-of-thought methods introduce discrete intermediate steps but lack a scalar measure of reasoning progress. We propose Energy-Based Reasoning via Structured Latent Planning (EBRM), which models reasoning as gradient-based optimization of a multi-step latent trajectory z_{1:T} under a learned energy function E(h_x, z). The energy decomposes into per-step compatibility, transition consistency, and trajectory smoothness terms. Training combines supervised encoder-decoder learning with contrastive energy shaping using hard negatives, while inference performs gradient descent or Langevin dynamics over z and decodes from z_T. We identify a critical failure mode: on CNF logic satisfaction, latent planning reduces accuracy from approx 95% to approx 56%. This degradation arises from a distribution mismatch, where the decoder is trained on encoder outputs h_x but evaluated on planner outputs z_T that drift into unseen latent regions. We analyze this behavior through per-step decoding, latent drift tracking, and gradient decomposition. To address it, we propose dual-path decoder training and latent anchoring. We further introduce a six-part ablation protocol covering component contributions, trajectory length, planner dynamics, initialization, decoder training distribution, and anchor weight. Experiments on three synthetic tasks show that energy decreases monotonically and induces structured latent trajectories on graph and logic tasks, while remaining flat on arithmetic (r = 0.073), indicating a negative result. Code is available at https://github.com/dkjo8/ebr-via-structured-latent-planning.

Identifying reliable synthesis pathways in materials chemistry is a complex task, particularly in polymer science, due to the intricate and often non-unique nomenclature of macromolecules. To address this challenge, we propose an agent system that integrates large language models (LLMs) and knowledge graphs (KGs). By leveraging LLMs' powerful capabilities for extracting and recognizing chemical substance names, and storing the extracted data in a structured knowledge graph, our system fully automates the retrieval of relevant literatures, extraction of reaction data, database querying, construction of retrosynthetic pathway trees, further expansion through the retrieval of additional literature and recommendation of optimal reaction pathways. A novel Multi-branched Reaction Pathway Search (MBRPS) algorithm enables the exploration of all pathways, with a particular focus on multi-branched ones, helping LLMs overcome weak reasoning in multi-branched paths. This work represents the first attempt to develop a fully automated retrosynthesis planning agent tailored specially for macromolecules powered by LLMs. Applied to polyimide synthesis, our new approach constructs a retrosynthetic pathway tree with hundreds of pathways and recommends optimized routes, including both known and novel pathways, demonstrating its effectiveness and potential for broader applications.

Computationally intensive decoding procedures--including search, reranking, and self-critique--can improve the quality of language model (LM) outputs in problems spanning code generation, numerical reasoning, and dialog. Existing work typically applies the same decoding procedure for every input to an LM. But not all inputs require the same amount of computation to process. Can we allocate decoding computation adaptively, using more resources to answer questions whose answers will be harder to compute? We present an approach that predicts the distribution of rewards given an input and computation budget, then allocates additional computation to inputs for which it is predicted to be most useful. We apply this approach in two decoding procedures: first, an adaptive best-of-k procedure that dynamically selects the number of samples to generate as input to a reranker; second, a routing procedure that dynamically responds to a query using a decoding procedure that is expensive but accurate, or one that is cheaper but less capable. Across a suite of programming, mathematics, and dialog tasks, we show that accurate computation-allocation procedures can be learned, and reduce computation by up to 50% at no cost to response quality, or improve quality by up to 10% at a fixed computational budget.

Scaling test-time compute with multi-path chain-of-thought improves reasoning accuracy, but its effectiveness depends critically on the exploration-exploitation trade-off. Existing approaches address this trade-off in rigid ways: tree-structured search hard-codes exploration through brittle expansion rules that interfere with post-trained reasoning, while parallel reasoning over-explores redundant hypothesis paths and relies on weak answer selection. Motivated by the observation that the optimal balance is phase-dependent and that correct and incorrect reasoning paths often diverge only at late stages, we reformulate test-time scaling as a dynamic expand-reduce control problem over a pool of hypotheses. We propose HyPER, a training-free online control policy for multi-path decoding in mixture-of-experts models that reallocates computation under a fixed budget using lightweight path statistics. HyPER consists of an online controller that transitions from exploration to exploitation as the hypothesis pool evolves, a token-level refinement mechanism that enables efficient generation-time exploitation without full-path resampling, and a length- and confidence-aware aggregation strategy for reliable answer-time exploitation. Experiments on four mixture-of-experts language models across diverse reasoning benchmarks show that HyPER consistently achieves a superior accuracy-compute trade-off, improving accuracy by 8 to 10 percent while reducing token usage by 25 to 40 percent.

While large language models have demonstrated exceptional performance across a wide range of tasks, they remain susceptible to hallucinations -- generating plausible yet factually incorrect contents. Existing methods to mitigating such risk often rely on sampling multiple full-length generations, which introduces significant response latency and becomes ineffective when the model consistently produces hallucinated outputs with high confidence. To address these limitations, we introduce Monitoring Decoding (MD), a novel framework that dynamically monitors the generation process and selectively applies in-process interventions, focusing on revising crucial tokens responsible for hallucinations. Instead of waiting until completion of multiple full-length generations, we identify hallucination-prone tokens during generation using a monitor function, and further refine these tokens through a tree-based decoding strategy. This approach ensures an enhanced factual accuracy and coherence in the generated output while maintaining efficiency. Experimental results demonstrate that MD consistently outperforms self-consistency-based approaches in both effectiveness and efficiency, achieving higher factual accuracy while significantly reducing computational overhead.

Neural machine translation (NMT) systems typically employ maximum a posteriori (MAP) decoding to select the highest-scoring translation from the distribution mass. However, recent evidence highlights the inadequacy of MAP decoding, often resulting in low-quality or even pathological hypotheses -- the decoding objective is not aligned with real-world translation quality. This paper proposes calibrating hypothesis likelihoods with translation quality from a distribution view by directly optimizing their Pearson correlation -- thereby enhancing the effectiveness of translation decoding. With our method, translation on large language models (LLMs) improves substantially after limited training (2K instances per direction). This improvement is orthogonal to those achieved through supervised fine-tuning, leading to substantial gains across a broad range of metrics and human evaluations -- even when applied to top-performing translation-specialized LLMs fine-tuned on high-quality translation data, such as Tower, or when compared to recent preference optimization methods, like CPO. Moreover, the calibrated translation likelihood can directly serve as a strong proxy for translation quality, closely approximating or even surpassing some state-of-the-art translation quality estimation models, like CometKiwi. Lastly, our in-depth analysis demonstrates that calibration enhances the effectiveness of MAP decoding, thereby enabling greater efficiency in real-world deployment. The resulting state-of-the-art translation model, which covers 10 languages, along with the accompanying code and human evaluation data, has been released to the community: https://github.com/moore3930/calibrating-llm-mt.

The "end-to-end" label for LLMs is a misnomer. In practice, they depend on a non-differentiable decoding process that requires laborious, hand-tuning of hyperparameters like temperature and top-p. This paper introduces AutoDeco, a novel architecture that enables truly "end-to-end" generation by learning to control its own decoding strategy. We augment the standard transformer with lightweight heads that, at each step, dynamically predict context-specific temperature and top-p values alongside the next-token logits. This approach transforms decoding into a parametric, token-level process, allowing the model to self-regulate its sampling strategy within a single forward pass. Through extensive experiments on eight benchmarks, we demonstrate that AutoDeco not only significantly outperforms default decoding strategies but also achieves performance comparable to an oracle-tuned baseline derived from "hacking the test set"-a practical upper bound for any static method. Crucially, we uncover an emergent capability for instruction-based decoding control: the model learns to interpret natural language commands (e.g., "generate with low randomness") and adjusts its predicted temperature and top-p on a token-by-token basis, opening a new paradigm for steerable and interactive LLM decoding.

We propose controlled decoding (CD), a novel off-policy reinforcement learning method to control the autoregressive generation from language models towards high reward outcomes. CD solves an off-policy reinforcement learning problem through a value function for the reward, which we call a prefix scorer. The prefix scorer is used at inference time to steer the generation towards higher reward outcomes. We show that the prefix scorer may be trained on (possibly) off-policy data to predict the expected reward when decoding is continued from a partially decoded response. We empirically demonstrate that CD is effective as a control mechanism on Reddit conversations corpus. We also show that the modularity of the design of CD makes it possible to control for multiple rewards, effectively solving a multi-objective reinforcement learning problem with no additional complexity. Finally, we show that CD can be applied in a novel blockwise fashion at inference-time, again without the need for any training-time changes, essentially bridging the gap between the popular best-of-K strategy and token-level reinforcement learning. This makes CD a promising approach for alignment of language models.

Transformers exhibit impressive capabilities but are often regarded as black boxes due to challenges in understanding the complex nonlinear relationships between features. Interpreting machine learning models is of paramount importance to mitigate risks, and mechanistic interpretability is in particular of current interest as it opens up a window for guiding manual modifications and reverse-engineering solutions. In this work, we introduce contextual decomposition for transformers (CD-T), extending a prior work on CD for RNNs and CNNs, to address mechanistic interpretation computationally efficiently. CD-T is a flexible interpretation method for transformers. It can capture contributions of combinations of input features or source internal components (e.g. attention heads, feed-forward networks) to (1) final predictions or (2) the output of any target internal component. Using CD-T, we propose a novel algorithm for circuit discovery. On a real-world pathology report classification task: we show CD-T distills a more faithful circuit of attention heads with improved computational efficiency (speed up 2x) than a prior benchmark, path patching. As a versatile interpretation method, CD-T also exhibits exceptional capabilities for local interpretations. CD-T is shown to reliably find words and phrases of contrasting sentiment/topic on SST-2 and AGNews datasets. Through human experiments, we demonstrate CD-T enables users to identify the more accurate of two models and to better trust a model's outputs compared to alternative interpretation methods such as SHAP and LIME.

Recent advancements in multimodal large reasoning models (MLRMs) have significantly improved performance in visual question answering. However, we observe that transition words (e.g., because, however, and wait) are closely associated with hallucinations and tend to exhibit high-entropy states. We argue that adequate contextual reasoning information can be directly extracted from the token probability distribution. Inspired by superposed representation theory, we propose leveraging latent superposed reasoning to integrate multiple candidate semantics and maintain latent reasoning trajectories. The hypothesis is that reliance on discrete textual inputs may drive the model toward sequential explicit reasoning, underutilizing dense contextual cues during high-entropy reasoning stages. Therefore, we propose constructing rich semantic representations from the token probability distributions to enhance in-context reasoning. With this goal, we present Latent Entropy-Aware Decoding (LEAD), an efficient plug-and-play decoding strategy that leverages semantic context to achieve reliable reasoning. The heart of our method lies in entropy-aware reasoning mode switching. The model employs probability-weighted continuous embeddings under high-entropy states and transitions back to discrete token embeddings as entropy decreases. Moreover, we propose a prior-guided visual anchor injection strategy that encourages the model to focus on visual information. Extensive experiments show that LEAD effectively mitigates hallucinations across various MLRMs on multiple benchmarks.

Transformer models underpin many recent advances in practical machine learning applications, yet understanding their internal behavior continues to elude researchers. Given the size and complexity of these models, forming a comprehensive picture of their inner workings remains a significant challenge. To this end, we set out to understand small transformer models in a more tractable setting: that of solving mazes. In this work, we focus on the abstractions formed by these models and find evidence for the consistent emergence of structured internal representations of maze topology and valid paths. We demonstrate this by showing that the residual stream of only a single token can be linearly decoded to faithfully reconstruct the entire maze. We also find that the learned embeddings of individual tokens have spatial structure. Furthermore, we take steps towards deciphering the circuity of path-following by identifying attention heads (dubbed adjacency heads), which are implicated in finding valid subsequent tokens.

Predicting spatial gene expression from H&E histology offers a scalable and clinically accessible alternative to sequencing, but realizing clinical impact requires models that generalize across cancer types and capture biologically coherent signals. Prior work is often limited to per-cancer settings and variance-based evaluation, leaving functional relevance underexplored. We introduce HistoPrism, an efficient transformer-based architecture for pan-cancer prediction of gene expression from histology. To evaluate biological meaning, we introduce a pathway-level benchmark, shifting assessment from isolated gene-level variance to coherent functional pathways. HistoPrism not only surpasses prior state-of-the-art models on highly variable genes , but also more importantly, achieves substantial gains on pathway-level prediction, demonstrating its ability to recover biologically coherent transcriptomic patterns. With strong pan-cancer generalization and improved efficiency, HistoPrism establishes a new standard for clinically relevant transcriptomic modeling from routinely available histology.

Deciphering visual content from functional Magnetic Resonance Imaging (fMRI) helps illuminate the human vision system. However, the scarcity of fMRI data and noise hamper brain decoding model performance. Previous approaches primarily employ subject-specific models, sensitive to training sample size. In this paper, we explore a straightforward but overlooked solution to address data scarcity. We propose shallow subject-specific adapters to map cross-subject fMRI data into unified representations. Subsequently, a shared deeper decoding model decodes cross-subject features into the target feature space. During training, we leverage both visual and textual supervision for multi-modal brain decoding. Our model integrates a high-level perception decoding pipeline and a pixel-wise reconstruction pipeline guided by high-level perceptions, simulating bottom-up and top-down processes in neuroscience. Empirical experiments demonstrate robust neural representation learning across subjects for both pipelines. Moreover, merging high-level and low-level information improves both low-level and high-level reconstruction metrics. Additionally, we successfully transfer learned general knowledge to new subjects by training new adapters with limited training data. Compared to previous state-of-the-art methods, notably pre-training-based methods (Mind-Vis and fMRI-PTE), our approach achieves comparable or superior results across diverse tasks, showing promise as an alternative method for cross-subject fMRI data pre-training. Our code and pre-trained weights will be publicly released at https://github.com/YulongBonjour/See_Through_Their_Minds.

Autoregressive transformer language models (LMs) possess strong syntactic abilities, often successfully handling phenomena from agreement to NPI licensing. However, the features they use to incrementally process language inputs are not well understood. In this paper, we fill this gap by studying the mechanisms underlying garden path sentence processing in LMs. We ask: (1) Do LMs use syntactic features or shallow heuristics to perform incremental sentence processing? (2) Do LMs represent only one potential interpretation, or multiple? and (3) Do LMs reanalyze or repair their initial incorrect representations? To address these questions, we use sparse autoencoders to identify interpretable features that determine which continuation - and thus which reading - of a garden path sentence the LM prefers. We find that while many important features relate to syntactic structure, some reflect syntactically irrelevant heuristics. Moreover, while most active features correspond to one reading of the sentence, some features correspond to the other, suggesting that LMs assign weight to both possibilities simultaneously. Finally, LMs do not re-use features from garden path sentence processing to answer follow-up questions.

Motivation: Biomedical knowledge graphs (KGs) are crucial for drug discovery and disease understanding, yet their completion and reasoning are challenging. Knowledge Embedding (KE) methods capture global semantics but struggle with dynamic structural integration, while Graph Neural Networks (GNNs) excel locally but often lack semantic understanding. Even ensemble approaches, including those leveraging language models, often fail to achieve a deep, adaptive, and synergistic co-evolution between semantic comprehension and structural learning. Addressing this critical gap in fostering continuous, reciprocal refinement between these two aspects in complex biomedical KGs is paramount. Results: We introduce BioGraphFusion, a novel framework for deeply synergistic semantic and structural learning. BioGraphFusion establishes a global semantic foundation via tensor decomposition, guiding an LSTM-driven mechanism to dynamically refine relation embeddings during graph propagation. This fosters adaptive interplay between semantic understanding and structural learning, further enhanced by query-guided subgraph construction and a hybrid scoring mechanism. Experiments across three key biomedical tasks demonstrate BioGraphFusion's superior performance over state-of-the-art KE, GNN, and ensemble models. A case study on Cutaneous Malignant Melanoma 1 (CMM1) highlights its ability to unveil biologically meaningful pathways. Availability and Implementation: Source code and all training data are freely available for download at https://github.com/Y-TARL/BioGraphFusion. Supplementary information: Supplementary data are available at Bioinformatics online.

Ever since neural models were adopted in data-to-text language generation, they have invariably been reliant on extrinsic components to improve their semantic accuracy, because the models normally do not exhibit the ability to generate text that reliably mentions all of the information provided in the input. In this paper, we propose a novel decoding method that extracts interpretable information from encoder-decoder models' cross-attention, and uses it to infer which attributes are mentioned in the generated text, which is subsequently used to rescore beam hypotheses. Using this decoding method with T5 and BART, we show on three datasets its ability to dramatically reduce semantic errors in the generated outputs, while maintaining their state-of-the-art quality.

Language models trained on large amounts of data require careful tuning to be safely deployed in real world. We revisit the guided decoding paradigm, where the goal is to augment the logits of the base language model using the scores from a task-specific reward model. We propose a simple but efficient parameterization of the autoregressive reward model enabling fast and effective guided decoding. On detoxification and sentiment control tasks, we show that our efficient parameterization performs on par with RAD, a strong but less efficient guided decoding approach.

Finding human-understandable circuits in language models is a central goal of the field of mechanistic interpretability. We train models to have more understandable circuits by constraining most of their weights to be zeros, so that each neuron only has a few connections. To recover fine-grained circuits underlying each of several hand-crafted tasks, we prune the models to isolate the part responsible for the task. These circuits often contain neurons and residual channels that correspond to natural concepts, with a small number of straightforwardly interpretable connections between them. We study how these models scale and find that making weights sparser trades off capability for interpretability, and scaling model size improves the capability-interpretability frontier. However, scaling sparse models beyond tens of millions of nonzero parameters while preserving interpretability remains a challenge. In addition to training weight-sparse models de novo, we show preliminary results suggesting our method can also be adapted to explain existing dense models. Our work produces circuits that achieve an unprecedented level of human understandability and validates them with considerable rigor.

Mechanistic interpretability seeks to understand the internal mechanisms of machine learning models, where localization -- identifying the important model components -- is a key step. Activation patching, also known as causal tracing or interchange intervention, is a standard technique for this task (Vig et al., 2020), but the literature contains many variants with little consensus on the choice of hyperparameters or methodology. In this work, we systematically examine the impact of methodological details in activation patching, including evaluation metrics and corruption methods. In several settings of localization and circuit discovery in language models, we find that varying these hyperparameters could lead to disparate interpretability results. Backed by empirical observations, we give conceptual arguments for why certain metrics or methods may be preferred. Finally, we provide recommendations for the best practices of activation patching going forwards.

Large Language Models (LLMs) are nowadays expected to generate content aligned with human preferences. Current work focuses on alignment at model training time, through techniques such as Reinforcement Learning with Human Feedback (RLHF). However, it is unclear if such methods are an effective choice to teach alignment objectives to the model. First, the inability to incorporate multiple, custom rewards and reliance on a model developer's view of universal and static principles are key limitations. Second, the residual gaps in model training and the reliability of such approaches are also questionable (e.g. susceptibility to jail-breaking even after safety training). To address these, we propose DeAL, a framework that allows the user to customize reward functions and enables Decoding-time Alignment of LLMs (DeAL). At its core, we view decoding as a heuristic-guided search process and facilitate the use of a wide variety of alignment objectives. Our experiments with programmatic constraints such as keyword and length constraints (studied widely in the pre-LLM era) and abstract objectives such as harmlessness and helpfulness (proposed in the post-LLM era) show that we can DeAL with fine-grained trade-offs, improve adherence to alignment objectives, and address residual gaps in LLMs. Lastly, while DeAL can be effectively paired with RLHF and prompting techniques, its generality makes decoding slower, an optimization we leave for future work.

Large Language Models (LLMs) are trained with next-token prediction, implemented in autoregressive Transformers via causal masking for parallelism. This creates a subtle misalignment: residual connections tie activations to the current token, while supervision targets the next token, potentially propagating mismatched information if the current token is not the most informative for prediction. In this work, we empirically localize this input-output alignment shift in pretrained LLMs, using decoding trajectories over tied embedding spaces and similarity-based metrics. Our experiments reveal that the hidden token representations switch from input alignment to output alignment deep within the network. Motivated by this observation, we propose a lightweight residual-path mitigation based on residual attenuation, implemented either as a fixed-layer intervention or as a learnable gating mechanism. Experiments on multiple benchmarks show that these strategies alleviate the representation misalignment and yield improvements, providing an efficient and general architectural enhancement for autoregressive Transformers.

Mechanistic interpretability aims to understand model behaviors in terms of specific, interpretable features, often hypothesized to manifest as low-dimensional subspaces of activations. Specifically, recent studies have explored subspace interventions (such as activation patching) as a way to simultaneously manipulate model behavior and attribute the features behind it to given subspaces. In this work, we demonstrate that these two aims diverge, potentially leading to an illusory sense of interpretability. Counterintuitively, even if a subspace intervention makes the model's output behave as if the value of a feature was changed, this effect may be achieved by activating a dormant parallel pathway leveraging another subspace that is causally disconnected from model outputs. We demonstrate this phenomenon in a distilled mathematical example, in two real-world domains (the indirect object identification task and factual recall), and present evidence for its prevalence in practice. In the context of factual recall, we further show a link to rank-1 fact editing, providing a mechanistic explanation for previous work observing an inconsistency between fact editing performance and fact localization. However, this does not imply that activation patching of subspaces is intrinsically unfit for interpretability. To contextualize our findings, we also show what a success case looks like in a task (indirect object identification) where prior manual circuit analysis informs an understanding of the location of a feature. We explore the additional evidence needed to argue that a patched subspace is faithful.

Diffusion large language models (DLLMs) have the potential to enable fast text generation by decoding multiple tokens in parallel. However, in practice, their inference efficiency is constrained by the need for many refinement steps, while aggressively reducing the number of steps leads to a substantial degradation in generation quality. To alleviate this, we propose a trajectory self-distillation framework that improves few-step decoding by distilling the model's own generative trajectories. We incorporate Direct Discriminative Optimization (DDO), a reverse-KL objective that promotes mode-seeking distillation and encourages the student to concentrate on high-probability teacher modes. Across benchmarks, our approach consistently outperforms strong few-step baselines and standard training under tight step budgets. Although full-step decoding remains superior, we substantially narrow the gap, establishing a strong foundation towards practical few-step DLLMs. The source code is available at https://github.com/Tyrion58/T3D.

The rapid progress of research aimed at interpreting the inner workings of advanced language models has highlighted a need for contextualizing the insights gained from years of work in this area. This primer provides a concise technical introduction to the current techniques used to interpret the inner workings of Transformer-based language models, focusing on the generative decoder-only architecture. We conclude by presenting a comprehensive overview of the known internal mechanisms implemented by these models, uncovering connections across popular approaches and active research directions in this area.

While most autoregressive LLMs are constrained to one-by-one decoding, diffusion LLMs (dLLMs) have attracted growing interest for their potential to dramatically accelerate inference through parallel decoding. Despite this promise, the conditional independence assumption in dLLMs causes parallel decoding to ignore token dependencies, inevitably degrading generation quality when these dependencies are strong. However, existing works largely overlook these inherent challenges, and evaluations on standard benchmarks (e.g., math and coding) are not sufficient to capture the quality degradation caused by parallel decoding. To address this gap, we first provide an information-theoretic analysis of parallel decoding. We then conduct case studies on analytically tractable synthetic list operations from both data distribution and decoding strategy perspectives, offering quantitative insights that highlight the fundamental limitations of parallel decoding. Building on these insights, we propose ParallelBench, the first benchmark specifically designed for dLLMs, featuring realistic tasks that are trivial for humans and autoregressive LLMs yet exceptionally challenging for dLLMs under parallel decoding. Using ParallelBench, we systematically analyze both dLLMs and autoregressive LLMs, revealing that: (i) dLLMs under parallel decoding can suffer dramatic quality degradation in real-world scenarios, and (ii) current parallel decoding strategies struggle to adapt their degree of parallelism based on task difficulty, thus failing to achieve meaningful speedup without compromising quality. Our findings underscore the pressing need for innovative decoding methods that can overcome the current speed-quality trade-off. We release our benchmark to help accelerate the development of truly efficient dLLMs.

Direct speech-to-speech translation (S2ST) translates speech from one language into another using a single model. However, due to the presence of linguistic and acoustic diversity, the target speech follows a complex multimodal distribution, posing challenges to achieving both high-quality translations and fast decoding speeds for S2ST models. In this paper, we propose DASpeech, a non-autoregressive direct S2ST model which realizes both fast and high-quality S2ST. To better capture the complex distribution of the target speech, DASpeech adopts the two-pass architecture to decompose the generation process into two steps, where a linguistic decoder first generates the target text, and an acoustic decoder then generates the target speech based on the hidden states of the linguistic decoder. Specifically, we use the decoder of DA-Transformer as the linguistic decoder, and use FastSpeech 2 as the acoustic decoder. DA-Transformer models translations with a directed acyclic graph (DAG). To consider all potential paths in the DAG during training, we calculate the expected hidden states for each target token via dynamic programming, and feed them into the acoustic decoder to predict the target mel-spectrogram. During inference, we select the most probable path and take hidden states on that path as input to the acoustic decoder. Experiments on the CVSS Fr-En benchmark demonstrate that DASpeech can achieve comparable or even better performance than the state-of-the-art S2ST model Translatotron 2, while preserving up to 18.53x speedup compared to the autoregressive baseline. Compared with the previous non-autoregressive S2ST model, DASpeech does not rely on knowledge distillation and iterative decoding, achieving significant improvements in both translation quality and decoding speed. Furthermore, DASpeech shows the ability to preserve the speaker's voice of the source speech during translation.

Neural decoding, a critical component of Brain-Computer Interface (BCI), has recently attracted increasing research interest. Previous research has focused on leveraging signal processing and deep learning methods to enhance neural decoding performance. However, the in-depth exploration of model architectures remains underexplored, despite its proven effectiveness in other tasks such as energy forecasting and image classification. In this study, we propose NeuroSketch, an effective framework for neural decoding via systematic architecture optimization. Starting with the basic architecture study, we find that CNN-2D outperforms other architectures in neural decoding tasks and explore its effectiveness from temporal and spatial perspectives. Building on this, we optimize the architecture from macro- to micro-level, achieving improvements in performance at each step. The exploration process and model validations take over 5,000 experiments spanning three distinct modalities (visual, auditory, and speech), three types of brain signals (EEG, SEEG, and ECoG), and eight diverse decoding tasks. Experimental results indicate that NeuroSketch achieves state-of-the-art (SOTA) performance across all evaluated datasets, positioning it as a powerful tool for neural decoding. Our code and scripts are available at https://github.com/Galaxy-Dawn/NeuroSketch.

Large language models (LLMs) have made remarkable strides in various natural language processing tasks, but their performance on complex reasoning problems remains hindered by a lack of explainability and trustworthiness. This issue, often manifesting as hallucinations or unattributable reasoning processes, limits their applicability in complex reasoning scenarios. To address this, we propose Knowledge Graph-constrained Trajectory Reasoning Attribution and Chain Explanation Supervision (KG-TRACES), a novel framework that enhances the reasoning ability of LLMs through explicit supervision over reasoning paths and processes. KG-TRACES jointly supervises the model to: (1) predict symbolic relation paths, (2) predict full triple-level reasoning paths, and (3) generate attribution-aware reasoning processes grounded in the reasoning paths. At inference phase, the model adapts to both KG-available and KG-unavailable scenarios, retrieving reasoning paths from a KG when possible or predicting plausible reasoning paths with only intrinsic knowledge when not. This design enables the model to reason in an explainable and source-attributable pattern. Through extensive experiments on complex reasoning tasks, we demonstrate that KG-TRACES significantly outperforms existing SOTA: it improves Hits@1 by 1.6% and F1 by 4.7% on WebQSP, and achieves improvements of 4.8% in Hits@1 and 2.1% in F1 on CWQ. Moreover, we show its transferability to specialized domains such as medicine. By visualizing the intermediate steps of reasoning processes, we further show that the explicit supervision introduced by KG-TRACES leads to more stable and goal-directed reasoning processes, aligning closely with correct answers. Code is available at https://github.com/Edaizi/KG-TRACES.

Despite remarkable advancements, current Text-to-Image (T2I) models struggle with complex, long-form textual instructions, frequently failing to accurately render intricate details, spatial relationships, or specific constraints. This limitation is highlighted by benchmarks such as LongBench-T2I, which reveal deficiencies in handling composition, specific text, and fine textures. To address this, we propose DeCoT (Decomposition-CoT), a novel framework that leverages Large Language Models (LLMs) to significantly enhance T2I models' understanding and execution of complex instructions. DeCoT operates in two core stages: first, Complex Instruction Decomposition and Semantic Enhancement, where an LLM breaks down raw instructions into structured, actionable semantic units and clarifies ambiguities; second, Multi-Stage Prompt Integration and Adaptive Generation, which transforms these units into a hierarchical or optimized single prompt tailored for existing T2I models. Extensive experiments on the LongBench-T2I dataset demonstrate that DeCoT consistently and substantially improves the performance of leading T2I models across all evaluated dimensions, particularly in challenging aspects like "Text" and "Composition". Quantitative results, validated by multiple MLLM evaluators (Gemini-2.0-Flash and InternVL3-78B), show that DeCoT, when integrated with Infinity-8B, achieves an average score of 3.52, outperforming the baseline Infinity-8B (3.44). Ablation studies confirm the critical contribution of each DeCoT component and the importance of sophisticated LLM prompting. Furthermore, human evaluations corroborate these findings, indicating superior perceptual quality and instruction fidelity. DeCoT effectively bridges the gap between high-level user intent and T2I model requirements, leading to more faithful and accurate image generation.

The practical utility of machine learning models in the sciences often hinges on their interpretability. It is common to assess a model's merit for scientific discovery, and thus novel insights, by how well it aligns with already available domain knowledge--a dimension that is currently largely disregarded in the comparison of neural network models. While pruning can simplify deep neural network architectures and excels in identifying sparse models, as we show in the context of gene regulatory network inference, state-of-the-art techniques struggle with biologically meaningful structure learning. To address this issue, we propose DASH, a generalizable framework that guides network pruning by using domain-specific structural information in model fitting and leads to sparser, better interpretable models that are more robust to noise. Using both synthetic data with ground truth information, as well as real-world gene expression data, we show that DASH, using knowledge about gene interaction partners within the putative regulatory network, outperforms general pruning methods by a large margin and yields deeper insights into the biological systems being studied.

Large Reasoning Models (LRMs) achieve remarkable inference-time improvements through parallel thinking. However, existing methods rely on redundant sampling of reasoning trajectories, failing to effectively explore the reasoning space to uncover high-quality solutions. To address these limitations, we propose Decoding Tree Sketching (DTS), a plug-and-play decoding framework for structural multi-trajectory exploration and reasoning selection. For reasoning exploration, DTS sketches a backbone tree of the reasoning space by selectively branching at decision tokens. For reasoning selection, guided by length-accuracy anti-correlation, DTS designs an early termination to prioritize short and reliable trajectories during decoding. Experimental results across four LRMs and datasets demonstrate that DTS significantly enhances accuracy by 14% and reduces repetitive generation by 8% on average. Notably, DTS enables smaller models to outperform larger models with 10times the size, highlighting its potential to strengthen reasoning capabilities.

Circuit analysis of any certain model behavior is a central task in mechanistic interpretability. We introduce our circuit discovery pipeline with Sparse Autoencoders (SAEs) and a variant called Transcoders. With these two modules inserted into the model, the model's computation graph with respect to OV and MLP circuits becomes strictly linear. Our methods do not require linear approximation to compute the causal effect of each node. This fine-grained graph identifies both end-to-end and local circuits accounting for either logits or intermediate features. We can scalably apply this pipeline with a technique called Hierarchical Attribution. We analyze three kinds of circuits in GPT-2 Small: bracket, induction, and Indirect Object Identification circuits. Our results reveal new findings underlying existing discoveries.

Efficiency, as a critical practical challenge for LLM-driven agentic and reasoning systems, is increasingly constrained by the inherent latency of autoregressive (AR) decoding. Speculative decoding mitigates this cost through a draft-verify scheme, yet existing approaches rely on AR draft models (a.k.a., drafters), which introduce two fundamental issues: (1) step-wise uncertainty accumulation leads to a progressive collapse of trust between the target model and the drafter, and (2) inherently sequential decoding of AR drafters. Together, these factors cause limited speedups. In this paper, we show that a diffusion large language model (dLLM) drafters can naturally overcome these issues through its fundamentally different probabilistic modeling and efficient parallel decoding strategy. Building on this insight, we introduce DEER, an efficient speculative decoding framework that drafts with diffusion and verifies with AR models. To enable high-quality drafting, DEER employs a two-stage training pipeline to align the dLLM-based drafters with the target AR model, and further adopts single-step decoding to generate long draft segments. Experiments show DEER reaches draft acceptance lengths of up to 32 tokens, far surpassing the 10 tokens achieved by EAGLE-3. Moreover, on HumanEval with Qwen3-30B-A3B, DEER attains a 5.54x speedup, while EAGLE-3 achieves only 2.41x. Code, model, demo, etc, will be available at https://czc726.github.io/DEER/

This technical report describes the design and training of novel speculative decoding draft models, for accelerating the inference speeds of large language models in a production environment. By conditioning draft predictions on both context vectors and sampled tokens, we can train our speculators to efficiently predict high-quality n-grams, which the base model then accepts or rejects. This allows us to effectively predict multiple tokens per inference forward pass, accelerating wall-clock inference speeds of highly optimized base model implementations by a factor of 2-3x. We explore these initial results and describe next steps for further improvements.

Stepwise inference protocols, such as scratchpads and chain-of-thought, help language models solve complex problems by decomposing them into a sequence of simpler subproblems. Despite the significant gain in performance achieved via these protocols, the underlying mechanisms of stepwise inference have remained elusive. To address this, we propose to study autoregressive Transformer models on a synthetic task that embodies the multi-step nature of problems where stepwise inference is generally most useful. Specifically, we define a graph navigation problem wherein a model is tasked with traversing a path from a start to a goal node on the graph. Despite is simplicity, we find we can empirically reproduce and analyze several phenomena observed at scale: (i) the stepwise inference reasoning gap, the cause of which we find in the structure of the training data; (ii) a diversity-accuracy tradeoff in model generations as sampling temperature varies; (iii) a simplicity bias in the model's output; and (iv) compositional generalization and a primacy bias with in-context exemplars. Overall, our work introduces a grounded, synthetic framework for studying stepwise inference and offers mechanistic hypotheses that can lay the foundation for a deeper understanding of this phenomenon.

Grokking, i.e., test performance keeps improving long after training loss converged, has been recently witnessed in neural network training, making the mechanism of generalization and other emerging capabilities such as reasoning mysterious. While prior studies usually train small models on a few toy or highly-specific tasks for thousands of epochs, we conduct the first study of grokking on checkpoints during one-pass pretraining of a 7B large language model (LLM), i.e., OLMoE. We compute the training loss and evaluate generalization on diverse benchmark tasks, including math reasoning, code generation, and commonsense/domain-specific knowledge retrieval tasks. Our study, for the first time, verifies that grokking still happens in the pretraining of large-scale foundation models, though different data may enter grokking stages asynchronously. We further demystify grokking's "emergence of generalization" by investigating LLM internal dynamics. Specifically, we find that training samples' pathways (i.e., expert choices across layers) evolve from random, instance-specific to more structured and shareable between samples during grokking. Also, the complexity of a sample's pathway reduces despite the converged loss. These indicate a memorization-to-generalization conversion, providing a mechanistic explanation of delayed generalization. In the study, we develop two novel metrics to quantify pathway distance and the complexity of a single pathway. We show their ability to predict the generalization improvement on diverse downstream tasks. They are efficient, simple to compute and solely dependent on training data. Hence, they have practical value for pretraining, enabling us to monitor the generalization performance without finetuning and test. Theoretically, we show that more structured pathways reduce model complexity and improve the generalization bound.

Diffusion Language Models (DLMs) present a promising non-sequential paradigm for text generation, distinct from standard autoregressive (AR) approaches. However, current decoding strategies often adopt a reactive stance, underutilizing the global bidirectional context to dictate global trajectories. To address this, we propose Plan-Verify-Fill (PVF), a training-free paradigm that grounds planning via quantitative validation. PVF actively constructs a hierarchical skeleton by prioritizing high-leverage semantic anchors and employs a verification protocol to operationalize pragmatic structural stopping where further deliberation yields diminishing returns. Extensive evaluations on LLaDA-8B-Instruct and Dream-7B-Instruct demonstrate that PVF reduces the Number of Function Evaluations (NFE) by up to 65% compared to confidence-based parallel decoding across benchmark datasets, unlocking superior efficiency without compromising accuracy.

Retrosynthetic planning aims to devise a complete multi-step synthetic route from starting materials to a target molecule. Current strategies use a decoupled approach of single-step retrosynthesis models and search algorithms, taking only the product as the input to predict the reactants for each planning step and ignoring valuable context information along the synthetic route. In this work, we propose a novel framework that utilizes context information for improved retrosynthetic planning. We view synthetic routes as reaction graphs and propose to incorporate context through three principled steps: encode molecules into embeddings, aggregate information over routes, and readout to predict reactants. Our approach is the first attempt to utilize in-context learning for retrosynthesis prediction in retrosynthetic planning. The entire framework can be efficiently optimized in an end-to-end fashion and produce more practical and accurate predictions. Comprehensive experiments demonstrate that by fusing in the context information over routes, our model significantly improves the performance of retrosynthetic planning over baselines that are not context-aware, especially for long synthetic routes. Code is available at https://github.com/SongtaoLiu0823/FusionRetro.

Knowledge Graphs (KGs) can serve as reliable knowledge sources for question answering (QA) due to their structured representation of knowledge. Existing research on the utilization of KG for large language models (LLMs) prevalently relies on subgraph retriever or iterative prompting, overlooking the potential synergy of LLMs' step-wise reasoning capabilities and KGs' structural nature. In this paper, we present DoG (Decoding on Graphs), a novel framework that facilitates a deep synergy between LLMs and KGs. We first define a concept, well-formed chain, which consists of a sequence of interrelated fact triplets on the KGs, starting from question entities and leading to answers. We argue that this concept can serve as a principle for making faithful and sound reasoning for KGQA. To enable LLMs to generate well-formed chains, we propose graph-aware constrained decoding, in which a constraint derived from the topology of the KG regulates the decoding process of the LLMs. This constrained decoding method ensures the generation of well-formed chains while making full use of the step-wise reasoning capabilities of LLMs. Based on the above, DoG, a training-free approach, is able to provide faithful and sound reasoning trajectories grounded on the KGs. Experiments across various KGQA tasks with different background KGs demonstrate that DoG achieves superior and robust performance. DoG also shows general applicability with various open-source LLMs.

Despite superior reasoning prowess demonstrated by Large Language Models (LLMs) with Chain-of-Thought (CoT) prompting, a lack of understanding prevails around the internal mechanisms of the models that facilitate CoT generation. This work investigates the neural sub-structures within LLMs that manifest CoT reasoning from a mechanistic point of view. From an analysis of LLaMA-2 7B applied to multistep reasoning over fictional ontologies, we demonstrate that LLMs deploy multiple parallel pathways of answer generation for step-by-step reasoning. These parallel pathways provide sequential answers from the input question context as well as the generated CoT. We observe a striking functional rift in the middle layers of the LLM. Token representations in the initial half remain strongly biased towards the pretraining prior, with the in-context taking over abruptly in the later half. This internal phase shift manifests in different functional components: attention heads that write the answer token predominantly appear in the later half, attention heads that move information along ontological relationships appear exclusively in the initial half, and so on. To the best of our knowledge, this is the first attempt towards mechanistic investigation of CoT reasoning in LLMs.

We present a conditional text generation framework that posits sentential expressions of possible causes and effects. This framework depends on two novel resources we develop in the course of this work: a very large-scale collection of English sentences expressing causal patterns CausalBank; and a refinement over previous work on constructing large lexical causal knowledge graphs Cause Effect Graph. Further, we extend prior work in lexically-constrained decoding to support disjunctive positive constraints. Human assessment confirms that our approach gives high-quality and diverse outputs. Finally, we use CausalBank to perform continued training of an encoder supporting a recent state-of-the-art model for causal reasoning, leading to a 3-point improvement on the COPA challenge set, with no change in model architecture.

Latent Chain-of-Thought (Latent-CoT) aims to enable step-by-step computation without emitting long rationales, yet its mechanisms remain unclear. We study CODI, a continuous-thought teacher-student distillation model, on strictly sequential polynomial-iteration tasks. Using logit-lens decoding, linear probes, attention analysis, and activation patching, we localize intermediate-state representations and trace their routing to the final readout. On two- and three-hop tasks, CODI forms the full set of bridge states that become decodable across latent-thought positions, while the final input follows a separate near-direct route; predictions arise via late fusion at the end-of-thought boundary. For longer hop lengths, CODI does not reliably execute a full latent rollout, instead exhibiting a partial latent reasoning path that concentrates on late intermediates and fuses them with the last input at the answer readout position. Ablations show that this partial pathway can collapse under regime shifts, including harder optimization. Overall, we delineate when CODI-style latent-CoT yields faithful iterative computation versus compressed or shortcut strategies, and highlight challenges in designing robust latent-CoT objectives for sequential reasoning.

We introduce Reward-Guided Speculative Decoding (RSD), a novel framework aimed at improving the efficiency of inference in large language models (LLMs). RSD synergistically combines a lightweight draft model with a more powerful target model, incorporating a controlled bias to prioritize high-reward outputs, in contrast to existing speculative decoding methods that enforce strict unbiasedness. RSD employs a process reward model to evaluate intermediate decoding steps and dynamically decide whether to invoke the target model, optimizing the trade-off between computational cost and output quality. We theoretically demonstrate that a threshold-based mixture strategy achieves an optimal balance between resource utilization and performance. Extensive evaluations on challenging reasoning benchmarks, including Olympiad-level tasks, show that RSD delivers significant efficiency gains against decoding with the target model only (up to 4.4x fewer FLOPs), while achieving significant better accuracy than parallel decoding method on average (up to +3.5). These results highlight RSD as a robust and cost-effective approach for deploying LLMs in resource-intensive scenarios.

Large language models (LLMs) exhibit strong reasoning abilities, often attributed to few-shot or zero-shot chain-of-thought (CoT) prompting. While effective, these methods require labor-intensive prompt engineering, raising the question of whether reasoning can be induced without reliance on explicit prompts. In this work, we unlock the reasoning capabilities of LLMs without explicit prompting. Inspired by zero-shot CoT and CoT-decoding, we propose a novel decoding strategy that systematically nudges LLMs to continue reasoning, thereby preventing immature reasoning processes. Specifically, we monitor the model's generation and inject a designated phrase whenever it is likely to conclude its response prematurely, before completing the reasoning process. Our experimental evaluations on diverse reasoning benchmarks demonstrate that our proposed strategy substantially improves LLM reasoning capabilities, highlighting the potential of decoding-based interventions as an alternative to traditional prompting techniques.

We propose NEURONA, a neuro-symbolic framework for fMRI decoding and concept grounding in neural activity. Leveraging image- and video-based fMRI question-answering datasets, NEURONA learns to decode interacting concepts from visual stimuli based on patterns of fMRI responses, integrating symbolic reasoning and compositional execution with fMRI grounding across brain regions. We demonstrate that incorporating structural priors (e.g., compositional predicate-argument dependencies between concepts) into the decoding process significantly improves both decoding accuracy over precise queries, and notably, generalization to unseen queries at test time. With NEURONA, we highlight neuro-symbolic frameworks as promising tools for understanding neural activity.

Large language models (LLMs) excel at generation but dominant autoregressive (AR) decoding is inherently sequential, creating a throughput bottleneck. Diffusion Language Models (DLMs)--especially block-wise variants--enable parallel generation and intra-block bidirectional reasoning, yet training large DLMs from scratch is costly and wastes the knowledge in mature AR checkpoints. Prior "adaptation" attempts either modify logits or randomly grow attention masks to full-sequence diffusion, or simply transplant AR weights into a block-diffusion recipe, leaving a fundamental mismatch between AR causality and block-wise bidirectionality unaddressed. We reframe adaptation as a intra-paradigm path from AR to Block-Diffusion by viewing AR as Block-Diffusion with blocksize=1. Concretely, we design the pathway of adaptation as follows: we use a context-causal attention mask (causal in context, bidirectional only within the active block), an efficient parallel adaptation procedure, an auxiliary AR loss to maximize data utilization and retain pretrained knowledge, and gradual increment of the generation block size. The recipe integrates cleanly with masked block-diffusion and maintains train-inference consistency. Built on these components, NBDiff-7B (Base and Instruct) could inherit the long-context modeling and reasoning capabilities, and achieve state-of-the-art performance among the 7B-class DLMs, delivering strong gains on general-knowledge, math, and code benchmarks over strong baselines. These results demonstrate that principled AR-to-block-diffusion adaptation is an effective and compute-efficient alternative to training DLMs from scratch. Codes: https://github.com/YuchuanTian/NBDiff.

Most efforts to improve the reasoning capabilities of large language models (LLMs) involve either scaling the number of parameters and the size of training data, or scaling inference computation by letting models generate complex chains of thought. Motivated by interpretability studies showing that the crucial computation required for reasoning tasks is concentrated in a limited range of layers, we introduce Encode-Think-Decode (ETD), a method that enhances the reasoning capabilities of a base model by training it to iterate over a small subset of reasoning-relevant layers during the mid-training stage. ETD amplifies latent reasoning while preserving the original architecture, parameter count, hyperparameters, and training data composition. When iterating on the selected layers at inference time, ETD models yield substantial gains on 17 reasoning benchmarks, including +28.4% relative accuracy improvement on GSM8K and +36% on MATH with the OLMo-2 1B Base model. We also explore an adaptive depth strategy that adjusts the computation per input token. Our results show that recursive latent reasoning offers a simple and effective path to stronger LLM reasoning.

Recent advances with large language models (LLM) illustrate their diverse capabilities. We propose a novel algorithm, staged speculative decoding, to accelerate LLM inference in small-batch, on-device scenarios. We address the low arithmetic intensity of small-batch inference by improving upon previous work in speculative decoding. First, we restructure the speculative batch as a tree, which reduces generation costs and increases the expected tokens per batch. Second, we add a second stage of speculative decoding. Taken together, we reduce single-batch decoding latency by 3.16x with a 762M parameter GPT-2-L model while perfectly preserving output quality.

Recently, Large Vision-Language Models (LVLMs) have demonstrated impressive capabilities in multi-modal context comprehension. However, they still suffer from hallucination problems referring to generating inconsistent outputs with the image content. To mitigate hallucinations, previous studies mainly focus on retraining LVLMs with custom datasets. Although effective, they inherently come with additional computational costs. In this paper, we propose a training-free framework, MVP, that aims to reduce hallucinations by making the most of the innate capabilities of the LVLMs via Multi-View Multi-Path Reasoning. Specifically, we first devise a multi-view information-seeking strategy to thoroughly perceive the comprehensive information in the image, which enriches the general global information captured by the original vision encoder in LVLMs. Furthermore, during the answer decoding, we observe that the occurrence of hallucinations has a strong correlation with the certainty of the answer tokens. Thus, we propose multi-path reasoning for each information view to quantify and aggregate the certainty scores for each potential answer among multiple decoding paths and finally decide the output answer. By fully grasping the information in the image and carefully considering the certainty of the potential answers when decoding, our MVP can effectively reduce hallucinations in LVLMs.The extensive experiments verify that our proposed MVP significantly mitigates the hallucination problem across four well-known LVLMs. The source code is available at: https://github.com/GasolSun36/MVP.

Text generation with beam search has proven successful in a wide range of applications. The commonly-used implementation of beam decoding follows a first come, first served heuristic: it keeps a set of already completed sequences over time steps and stops when the size of this set reaches the beam size. We introduce a patience factor, a simple modification to this decoding algorithm, that generalizes the stopping criterion and provides flexibility to the depth of search. Extensive empirical results demonstrate that the patience factor improves decoding performance of strong pretrained models on news text summarization and machine translation over diverse language pairs, with a negligible inference slowdown. Our approach only modifies one line of code and can be thus readily incorporated in any implementation.

Language and vision-language models have shown impressive performance across a wide range of tasks, but their internal mechanisms remain only partly understood. In this work, we study how individual attention heads in text-generative models specialize in specific semantic or visual attributes. Building on an established interpretability method, we reinterpret the practice of probing intermediate activations with the final decoding layer through the lens of signal processing. This lets us analyze multiple samples in a principled way and rank attention heads based on their relevance to target concepts. Our results show consistent patterns of specialization at the head level across both unimodal and multimodal transformers. Remarkably, we find that editing as few as 1% of the heads, selected using our method, can reliably suppress or enhance targeted concepts in the model output. We validate our approach on language tasks such as question answering and toxicity mitigation, as well as vision-language tasks including image classification and captioning. Our findings highlight an interpretable and controllable structure within attention layers, offering simple tools for understanding and editing large-scale generative models.

Automatic Speech Recognition (ASR) has seen remarkable progress, with models like OpenAI Whisper and NVIDIA Canary achieving state-of-the-art (SOTA) performance in offline transcription. However, these models are not designed for streaming (online or real-time) transcription, due to limitations in their architecture and training methodology. We propose a method to turn the transformer encoder-decoder model into a low-latency streaming model that is careless about future context. We present an analysis explaining why it is not straightforward to convert an encoder-decoder transformer to a low-latency streaming model. Our proposed method modifies the existing (non-causal) encoder to a causal encoder by fine-tuning both the encoder and decoder using Low-Rank Adaptation (LoRA) and a weakly aligned dataset. We then propose an updated inference mechanism that utilizes the fine-tune causal encoder and decoder to yield greedy and beam-search decoding, and is shown to be locally optimal. Experiments on low-latency chunk sizes (less than 300 msec) show that our fine-tuned model outperforms existing non-fine-tuned streaming approaches in most cases, while using a lower complexity. Additionally, we observe that our training process yields better alignment, enabling a simple method for extracting word-level timestamps. We release our training and inference code, along with the fine-tuned models, to support further research and development in streaming ASR.

Speculative decoding (SD) accelerates large language model inference by using a smaller draft model to predict multiple tokens, which are then verified in parallel by the larger target model. However, the limited capacity of the draft model often necessitates tree-based sampling to improve prediction accuracy, where multiple candidates are generated at each step. We identify a key limitation in this approach: the candidates at the same step are derived from the same representation, limiting diversity and reducing overall effectiveness. To address this, we propose Jakiro, leveraging Mixture of Experts (MoE), where independent experts generate diverse predictions, effectively decoupling correlations among candidates. Furthermore, we introduce a hybrid inference strategy, combining autoregressive decoding for initial tokens with parallel decoding for subsequent stages, and enhance the latter with contrastive mechanism in features to improve accuracy. Our method significantly boosts prediction accuracy and achieves higher inference speedups. Extensive experiments across diverse models validate the effectiveness and robustness of our approach, establishing a new SOTA in speculative decoding. Our codes are available at https://github.com/haiduo/Jakiro.

Inference-time scaling has emerged as a powerful alternative to parameter scaling for improving language model performance on complex reasoning tasks. While existing methods have shown strong performance gains under fixed compute budgets, there has been little focus on optimally utilizing that budget during inference. In this work, we introduce A*-decoding, a search-based inference-time strategy that builds on the A* search algorithm to optimally utilize a fixed compute budget by prioritizing high-quality reasoning paths during generation. We frame language model decoding as a structured search in a state space of partial solutions, applying the A* transition model to identify promising continuations guided by an external process supervision signal. In our experiments, A*-decoding reaches the performance levels of strong inference scaling baselines like best-of-N and particle filtering while using up to 3x fewer tokens and 30% fewer PRM passes under equivalent compute budgets. On the MATH500 and AIME 2024 benchmarks, A*-decoding enables Llama-3.2-1B-Instruct to match the performance of the 70x larger Llama-3.1-70B-Instruct, and allows Qwen3-1.7B to reach o1-like reasoning accuracy. These results highlight the power of structured search in decoding, offering an alternative to brute-force sampling or scale-driven gains. Our work demonstrates how thoughtful inference-time strategies can enhance reasoning in SLMs, pointing toward future advances in more efficient and scalable language model deployment.

Large language models have demonstrated exceptional capability in natural language understanding and generation. However, their generation speed is limited by the inherently sequential nature of their decoding process, posing challenges for real-time applications. This paper introduces Lexical Unit Decoding (LUD), a novel decoding methodology implemented in a data-driven manner, accelerating the decoding process without sacrificing output quality. The core of our approach is the observation that a pre-trained language model can confidently predict multiple contiguous tokens, forming the basis for a lexical unit, in which these contiguous tokens could be decoded in parallel. Extensive experiments validate that our method substantially reduces decoding time while maintaining generation quality, i.e., 33\% speed up on natural language generation with no quality loss, and 30\% speed up on code generation with a negligible quality loss of 3\%. Distinctively, LUD requires no auxiliary models and does not require changes to existing architectures. It can also be integrated with other decoding acceleration methods, thus achieving an even more pronounced inference efficiency boost. We posit that the foundational principles of LUD could define a new decoding paradigm for future language models, enhancing their applicability for a broader spectrum of applications. All codes are be publicly available at https://github.com/tjunlp-lab/Lexical-Unit-Decoding-LUD-. Keywords: Parallel Decoding, Lexical Unit Decoding, Large Language Model

In this paper, we introduce agentic unlearning which removes specified information from both model parameters and persistent memory in agents with closed-loop interaction. Existing unlearning methods target parameters alone, leaving two critical gaps: (i) parameter-memory backflow, where retrieval reactivates parametric remnants or memory artifacts reintroduce sensitive content, and (ii) the absence of a unified strategy that covers both parameter and memory pathways. We present Synchronized Backflow Unlearning (SBU), a framework that unlearns jointly across parameter and memory pathways. The memory pathway performs dependency closure-based unlearning that prunes isolated entities while logically invalidating shared artifacts. The parameter pathway employs stochastic reference alignment to guide model outputs toward a high-entropy prior. These pathways are integrated via a synchronized dual-update protocol, forming a closed-loop mechanism where memory unlearning and parametric suppression reinforce each other to prevent cross-pathway recontamination. Experiments on medical QA benchmarks show that SBU reduces traces of targeted private information across both pathways with limited degradation on retained data.

Chain-of-thought (CoT) decoding enables language models to improve reasoning performance at the cost of high generation latency in decoding. Recent proposals have explored variants of contemplation tokens, a term we introduce that refers to special tokens used during inference to allow for extra computation. Prior work has considered fixed-length sequences drawn from a discrete set of embeddings as contemplation tokens. Here we propose Compressed Chain-of-Thought (CCoT), a framework to generate contentful and continuous contemplation tokens of variable sequence length. The generated contemplation tokens are compressed representations of explicit reasoning chains, and our method can be applied to off-the-shelf decoder language models. Through experiments, we illustrate how CCoT enables additional reasoning over dense contentful representations to achieve corresponding improvements in accuracy. Moreover, the reasoning improvements can be adaptively modified on demand by controlling the number of contemplation tokens generated.

Query-focused summarization (QFS) aims to provide a summary of a single document/multi documents that can satisfy the information needs of a given query. It is useful for various real-world applications, such as abstractive snippet generation or more recent retrieval augmented generation (RAG). A prototypical QFS pipeline consists of a retriever (sparse or dense retrieval) and a generator (usually a large language model). However, applying large language models (LLM) potentially leads to hallucinations, especially when the evidence contradicts the prior belief of LLMs. There has been growing interest in developing new decoding methods to improve generation quality and reduce hallucination. In this work, we conduct a large-scale reproducibility study on one recently proposed decoding method -- Context-aware Decoding (CAD). In addition to replicating CAD's experiments on news summarization datasets, we include experiments on QFS datasets, and conduct more rigorous analysis on computational complexity and hyperparameter sensitivity. Experiments with eight different language models show that performance-wise, CAD improves QFS quality by (1) reducing factuality errors/hallucinations while (2) mostly retaining the match of lexical patterns, measured by ROUGE scores, while also at a cost of increased inference-time FLOPs and reduced decoding speed. The code implementation based on Huggingface Library is made available https://github.com/zhichaoxu-shufe/context-aware-decoding-qfs