Relaxing Positional Alignment in Masked Diffusion Language Models

Masked diffusion language models (MDLMs) have emerged as a promising alternative to dominant autoregressive approaches. Although they achieve competitive performance on several tasks, a substantial gap remains in open-ended text generation. We hypothesize that one cause of this gap is that strict positional prediction makes MDLM decoding highly sensitive to token misalignment, and we show through controlled interventions that a one-position shift can severely disrupt semantics. This observation suggests that enforcing strict positional supervision during training is misaligned with the irreversible denoising dynamics of MDLM decoding. Motivated by this mismatch, we adopt an alignment-flexible supervision strategy during fine-tuning. Specifically, we introduce a special token <slack> via the connectionist temporal classification objective. We apply this approach to the widely used MDLM model and conduct experiments on five open-ended text generation benchmarks. Our method consistently outperforms the original model and improves robustness to positional shifts, indicating that relaxing strict positional supervision is an important factor in improving generation quality in MDLMs.

TimeMachine-bench: A Benchmark for Evaluating Model Capabilities in Repository-Level Migration Tasks

With the advancement of automated software engineering, research focus is increasingly shifting toward practical tasks reflecting the day-to-day work of software engineers. Among these tasks, software migration, a critical process of adapting code to evolving environments, has been largely overlooked. In this study, we introduce TimeMachine-bench, a benchmark designed to evaluate software migration in real-world Python projects. Our benchmark consists of GitHub repositories whose tests begin to fail in response to dependency updates. The construction process is fully automated, enabling live updates of the benchmark. Furthermore, we curated a human-verified subset to ensure problem solvability. We evaluated agent-based baselines built on top of 11 models, including both strong open-weight and state-of-the-art LLMs on this verified subset. Our results indicated that, while LLMs show some promise for migration tasks, they continue to face substantial reliability challenges, including spurious solutions that exploit low test coverage and unnecessary edits stemming from suboptimal tool-use strategies. Our dataset and implementation are available at https://github.com/tohoku-nlp/timemachine-bench.

Suppressing Final Layer Hidden State Jumps in Transformer Pretraining

This paper discusses the internal behavior of Transformer language models. Many recent pre-trained models have been reported to exhibit only slight changes in the angular distance between the input and output hidden state vectors in the middle Transformer layers, despite a disproportionately large ``jump'' in the angular distance occurring in or around the final Transformer layer. To characterize this, we first introduce a quantitative metric for the jump strength around the final layer, and then demonstrate its prevalence across many open-weight models, as well as its amplification throughout pre-training. Assuming such jumps indicate an undesirable property, we propose the jump-suppressing regularizer (JREG) which penalizes this jump during pre-training, thereby encouraging more balanced capability usage across the middle layers. Empirical evaluations of three model sizes of Llama-based models, trained with the proposed JREG method, reveal improved task performance compared to the baseline without altering the model architecture.

Instruction-Following Evaluation of Large Vision-Language Models

Following the initial flourishing of large language models (LLMs), there has been a surge in proposed large vision-language models (LVLMs) that integrate LLMs with vision capabilities. However, it has been observed that LVLMs, after tuning to visual instruction using commonly used training datasets, often fail to exhibit the instruction-following ability that was present in the LLM before integration, leading to results in which they do not follow task instructions as expected. This study quantitatively demonstrates that LVLMs' instruction-following ability declines after fine-tuning and analyzes its underlying causes. In particular, we constructed new training datasets highlighting whether the output format is specified. Then, we investigated how explicitly indicating the output format during fine-tuning affects LVLMs' instruction-following ability. Our quantitative evaluation confirmed that LVLMs' instruction-following ability declines after fine-tuning with commonly used datasets. Furthermore, we found that LVLMs trained with datasets, including instructions on output format, tend to follow instructions more accurately than models that do not. These findings suggest that including samples with instructions on output format during (visual) instruction tuning may help mitigate the decline in instruction-following abilities.

An Open and Reproducible Deep Research Agent for Long-Form Question Answering

We present an open deep research system for long-form question answering, selected as a winning system in the text-to-text track of the MMU-RAG competition at NeurIPS 2025. The system combines an open-source large language model (LLM) with an open web search API to perform iterative retrieval, reasoning, and synthesis in real-world open-domain settings. To enhance reasoning quality, we apply preference tuning based on LLM-as-a-judge feedback that evaluates multiple aspects, including clarity, insightfulness, and factuality. Our experimental results show that the proposed method consistently improves answer quality across all three aspects. Our source code is publicly available at https://github.com/efficient-deep-research/efficient-deep-research.

Transformer Key-Value Memories Are Nearly as Interpretable as Sparse Autoencoders

Recent interpretability work on large language models (LLMs) has been increasingly dominated by a feature-discovery approach with the help of proxy modules. Then, the quality of features learned by, e.g., sparse auto-encoders (SAEs), is evaluated. This paradigm naturally raises a critical question: do such learned features have better properties than those already represented within the original model parameters, and unfortunately, only a few studies have made such comparisons systematically so far. In this work, we revisit the interpretability of feature vectors stored in feed-forward (FF) layers, given the perspective of FF as key-value memories, with modern interpretability benchmarks. Our extensive evaluation revealed that SAE and FFs exhibits a similar range of interpretability, although SAEs displayed an observable but minimal improvement in some aspects. Furthermore, in certain aspects, surprisingly, even vanilla FFs yielded better interpretability than the SAEs, and features discovered in SAEs and FFs diverged. These bring questions about the advantage of SAEs from both perspectives of feature quality and faithfulness, compared to directly interpreting FF feature vectors, and FF key-value parameters serve as a strong baseline in modern interpretability research.

Optimal Sparsity of Mixture-of-Experts Language Models for Reasoning Tasks

Empirical scaling laws have driven the evolution of large language models (LLMs), yet their coefficients shift whenever the model architecture or data pipeline changes. Mixture-of-Experts (MoE) models, now standard in state-of-the-art systems, introduce a new sparsity dimension that current dense-model frontiers overlook. We investigate how MoE sparsity influences two distinct capability regimes: memorization and reasoning. We train families of MoE Transformers that systematically vary total parameters, active parameters, and top-$k$ routing while holding the compute budget fixed. For every model we record pre-training loss, downstream task loss, and task accuracy, allowing us to separate the train-test generalization gap from the loss-accuracy gap. Memorization benchmarks improve monotonically with total parameters, mirroring training loss. By contrast, reasoning performance saturates and can even regress despite continued gains in both total parameters and training loss. Altering top-$k$ alone has little effect when active parameters are constant, and classic hyperparameters such as learning rate and initialization modulate the generalization gap in the same direction as sparsity. Neither post-training reinforcement learning (GRPO) nor extra test-time compute rescues the reasoning deficit of overly sparse models. Our model checkpoints, code and logs are open-source at https://github.com/rioyokotalab/optimal-sparsity.

Layerwise Importance Analysis of Feed-Forward Networks in Transformer-based Language Models

This study investigates the layerwise importance of feed-forward networks (FFNs) in Transformer-based language models during pretraining. We introduce an experimental approach that, while maintaining the total parameter count, increases the FFN dimensions in some layers and completely removes the FFNs from other layers. Furthermore, since our focus is on the importance of FFNs during pretraining, we train models from scratch to examine whether the importance of FFNs varies depending on their layer positions, rather than using publicly available pretrained models as is frequently done. Through comprehensive evaluations of models with varying sizes (285M, 570M, and 1.2B parameters) and layer counts (12, 24, and 40 layers), we demonstrate that concentrating FFNs in 70% of the consecutive middle layers consistently outperforms standard configurations for multiple downstream tasks.

VDocRAG: Retrieval-Augmented Generation over Visually-Rich Documents

We aim to develop a retrieval-augmented generation (RAG) framework that answers questions over a corpus of visually-rich documents presented in mixed modalities (e.g., charts, tables) and diverse formats (e.g., PDF, PPTX). In this paper, we introduce a new RAG framework, VDocRAG, which can directly understand varied documents and modalities in a unified image format to prevent missing information that occurs by parsing documents to obtain text. To improve the performance, we propose novel self-supervised pre-training tasks that adapt large vision-language models for retrieval by compressing visual information into dense token representations while aligning them with textual content in documents. Furthermore, we introduce OpenDocVQA, the first unified collection of open-domain document visual question answering datasets, encompassing diverse document types and formats. OpenDocVQA provides a comprehensive resource for training and evaluating retrieval and question answering models on visually-rich documents in an open-domain setting. Experiments show that VDocRAG substantially outperforms conventional text-based RAG and has strong generalization capability, highlighting the potential of an effective RAG paradigm for real-world documents.

STEP: Staged Parameter-Efficient Pre-training for Large Language Models

Pre-training large language models (LLMs) faces significant memory challenges due to the large size of model parameters. We introduce STaged parameter-Efficient Pre-training (STEP), which integrates parameter-efficient tuning techniques with model growth. We conduct experiments on pre-training LLMs of various sizes and demonstrate that STEP achieves up to a 53.9% reduction in maximum memory requirements compared to vanilla pre-training while maintaining equivalent performance. Furthermore, we show that the model by STEP performs comparably to vanilla pre-trained models on downstream tasks after instruction tuning.