POSPAN: Position-Constrained Span Masking for Language Model Pre-training

Masked diffusion language models (MDLMs) enable parallel generation and bidirectional context modeling, but their positional context differs fundamentally from that of autoregressive (AR) models. Whereas AR decoding exposes a contiguous prefix, MDLM denoising produces dynamic, non-contiguous configurations of revealed and masked tokens. Conventional positional encodings such as RoPE capture sequence order and pairwise displacement but remain insensitive to this evolving token-availability structure. To address this limitation, we propose MDLMPE, a positional encoding designed specifically for masked diffusion. To the best of our knowledge, MDLMPE is the first method to make positional representations explicitly aware of the changing revealed/masked configuration. It represents token availability as a binary sequence, applies distance-aware Gaussian weighting, and projects the resulting pattern through a cosine basis to obtain distribution-aware positional features. These features are added to token embeddings and mapped by a lightweight MLP to angular offsets that modulate the standard RoPE phases. Extensive experiments on LLaDA and DREAM demonstrate that MDLMPE generally outperforms conventional positional encoding methods across supervised fine-tuning, pretraining, zero-shot evaluation, and block-diffusion settings. Further ablations show that the complete combination of availability state, Gaussian locality, spectral basis, and embedding injection yields the strongest result. These results establish the evolving token-availability distribution as a useful positional signal for masked diffusion language models.

The choice of which tokens to mask is an under-examined design decision in masked language modeling (MLM). Standard pretraining masks tokens uniformly at random, whereas content-aware masking schemes can improve downstream transfer. We study masking as a task-adaptive component of the fine-tuning pipeline and introduce Typhoon, a masking strategy that uses the gradient of the MLM loss with respect to one-hot token inputs to estimate online how much each token type contributes to the objective. Typhoon maintains an exponential moving average of per-token-type saliency and calibrates these scores into a masking distribution whose expected masking rate matches a target budget under a token-independence approximation. We formalize the method and evaluate it against random masking and whole-word masking on two GLUE tasks, MRPC and CoLA, across three BERT-family backbones (TinyBERT, DistilBERT, and BERT-base) and five random seeds per configuration ($90$ training runs in total). Once seed variance is accounted for, no masking strategy is reliably better than the others on these tasks: on MRPC the gap between Typhoon and the best baseline stays within $0.004$ $F_1$, across all twelve Typhoon comparisons no paired test reaches significance, and every $95\%$ confidence interval contains zero. Inspecting Typhoon's learned distribution explains why: budget-preserving min-max calibration compresses the gradient ranking into a narrow band whose Kullback-Leibler divergence from uniform random masking is $7\times 10^{-4}$ nats per token, and widening the calibration spread by an order of magnitude in KL still leaves downstream accuracy unchanged within seed noise. Typhoon's apparent advantage in single-run experiments does not survive multi-seed evaluation, showing that gradient-based task-adaptive masking is competitive with, but does not outperform, uniform random masking at this scale.

Protein language models are trained primarily with masked language modeling (MLM), which predicts masked amino-acid identities. Joint-embedding predictive architectures (JEPA) instead predict latent representations, but have not been applied to proteins. ProteinJEPA supplements MLM with a cosine loss for predicting the half-depth hidden states of a teacher given the unmasked sequence. On 19 tasks, with ESM2 at 35M and 150M parameters and three pretraining seeds, MLM+JEPA outperforms compute-matched and step-matched MLM-only continued training in 78 and 76 of 114 comparisons (14 losses, 22 ties). The median compute-matched gain is $+0.0106$ on structure- and homology-sensitive tasks versus $+0.0041$ elsewhere, led by SCOPe-40 retrieval and remote homology with improvements of 6.1 percentage points in Recall@1 and 2.7 points in accuracy, respectively. Gains on these tasks increase with model size from 8M to 150M. Against the off-the-shelf checkpoint, MLM+JEPA wins 81 of 114 comparisons (median $+0.0068$) without improving MLM loss. In random initialization the gain is smaller and replicates inconsistently across seeds ($p{=}0.059$). The same recipe improves the causal ProGen3 model, beating a compute-matched next-token-prediction control on 12 of 16 tasks. Ablations show that cosine loss beats mean squared error, while adding shallower targets removes most of the task gain. JEPA-only training collapses downstream performance: latent prediction complements MLM rather than replacing it. Code: https://anonymous.4open.science/r/protJepa-FF24