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Jul 28

MarkushGrapher: Joint Visual and Textual Recognition of Markush Structures

The automated analysis of chemical literature holds promise to accelerate discovery in fields such as material science and drug development. In particular, search capabilities for chemical structures and Markush structures (chemical structure templates) within patent documents are valuable, e.g., for prior-art search. Advancements have been made in the automatic extraction of chemical structures from text and images, yet the Markush structures remain largely unexplored due to their complex multi-modal nature. In this work, we present MarkushGrapher, a multi-modal approach for recognizing Markush structures in documents. Our method jointly encodes text, image, and layout information through a Vision-Text-Layout encoder and an Optical Chemical Structure Recognition vision encoder. These representations are merged and used to auto-regressively generate a sequential graph representation of the Markush structure along with a table defining its variable groups. To overcome the lack of real-world training data, we propose a synthetic data generation pipeline that produces a wide range of realistic Markush structures. Additionally, we present M2S, the first annotated benchmark of real-world Markush structures, to advance research on this challenging task. Extensive experiments demonstrate that our approach outperforms state-of-the-art chemistry-specific and general-purpose vision-language models in most evaluation settings. Code, models, and datasets will be available.

  • 7 authors
·
Mar 20, 2025

Exact Regular-Constrained Variable-Order Markov Generation via Sparse Context-State Belief Propagation

Variable-order Markov models generate sequences over a finite alphabet by conditioning each symbol on the longest available suffix of the generated history. Regular constraints, by contrast, describe finite-horizon control requirements by an automaton: fixed positions, forced endings, metrical patterns, and forbidden copied fragments are all special cases. Existing exact methods already handle regular constraints with belief propagation for first-order Markov chains. The contribution here is the variable-order extension: identifying the state space on which the existing BP-regular machinery must be run when the generator is a variable-order/backoff model. A first-order constraint layer can enforce useful support conditions, but it computes future mass after merging histories that a variable-order generator deliberately keeps distinct. We formalize this mismatch and give the sparse construction obtained by replacing the first-order Markov state with the observed context state, then taking the standard product with the regular constraint automaton. For a fixed trained context graph and automaton, inference is linear in the sequence horizon; in general it is polynomial in the number of reachable product edges. This gives the correct variable-order distribution conditioned on regular constraints without expanding to all K-tuples. The same finite-source interface supports reversible data augmentation by inverse count lookup, matching materialized transposition augmentation without storing transformed corpora. We also separate exact BP inference from generation-time backoff policies, such as singleton avoidance, whose stochastic semantics must be made explicit if exactness is claimed.

  • 1 authors
·
May 7

AIFS-SUBS: Extending Data-Driven Forecasting to Sub-Seasonal Timescales

Data-driven models now rival numerical weather prediction in the medium range, but extending them to sub-seasonal lead times raises challenges absent at shorter horizons. Errors accumulate over long autoregressive rollouts, systematic biases grow with lead time, and several years of data must be held out for independent verification, even though machine-learning models otherwise benefit from longer training records. To address these challenges, we adapt ECMWF's AIFS-CRPS medium-range model. AIFS-SUBS adopts a 24h autoregressive time step to reduce error accumulation, adds stratospheric levels and top-of-atmosphere thermal radiation as predictors, and reserves 2007--2011 as an independent verification window. We evaluate two config-durations: AIFS-SUBS, fine-tuned on operational analyses, and AIFS-SUBS-ERA5, trained on ERA5 alone. Across weeks 2--6, AIFS-SUBS matches the operational Integrated Forecasting System (IFS) in probabilistic skill while reducing systematic biases. For the convective (OLR) component of the Madden--Julian Oscillation (MJO), AIFS-SUBS extends skilful forecasts (correlation > 0.5) by eight days relative to the IFS, while matching or exceeding the IFS for the full multivariate RMM index. AIFS-SUBS also reproduces the observed MJO modulation of tropical cyclone activity comparably. Stratospheric skill is particularly strong with AIFS-SUBS reproducing sudden stratospheric warming (SSW) frequency and surface impact. In the AI Weather Quest, AIFS-SUBS-ERA5 attains a variable-averaged ranked probability skill score slightly ahead of the IFS at weeks 3 and 4. At inference, AIFS-SUBS uses about 200 times less energy than the IFS, opening the door to much larger real-time ensembles. AIFS-SUBS is ECMWF's first machine-learning model targeted at sub-seasonal time-scales.

  • 9 authors
·
Jul 5

TempoVLA: Learning Speed-Controllable Vision-Language-Action Policies

Robot manipulation alternates between low-risk transit phases that call for fast execution and high-risk contact stages that demand slow, precise motion. Yet existing Vision-Language-Action models (VLAs) only inherit a single fixed speed from training demonstrations. Prior efforts to accelerate VLAs through model compression, KV-cache reuse, or reinforcement learning only shift the policy from one fixed speed to another, and leave deceleration almost unexplored. We observe that the magnitude of each predicted action already governs how fast the robot moves, opening a direct route to controllable execution speed. We turn this observation into TempoVLA, a single VLA whose execution speed is controlled by an explicit condition. TempoVLA combines two coupled components. (1) A data-side Variable-Speed Trajectory Augmentation (VSTA) that re-times demonstration to any target speed by merging or splitting actions while preserving its motion semantics. (2) A model-side conditioning mechanism that feeds the speed to the policy. Statistics show that VSTA reaches the requested speed with negligible motion error. Experiments in simulation and on real-world tasks demonstrate that TempoVLA achieves flexible speed control in both directions, while VSTA additionally boosts the default 1times performance via better data utilization. Furthermore, by cooperating with a large multimodal model, TempoVLA realizes dynamic speed control, accelerating through low-risk phases and decelerating for high-risk ones.

  • 7 authors
·
Jun 3