Daily Papers

mRNA-based vaccines have become a major focus in the pharmaceutical industry. The coding sequence as well as the Untranslated Regions (UTRs) of an mRNA can strongly influence translation efficiency, stability, degradation, and other factors that collectively determine a vaccine's effectiveness. However, optimizing mRNA sequences for those properties remains a complex challenge. Existing deep learning models often focus solely on coding region optimization, overlooking the UTRs. We present Helix-mRNA, a structured state-space-based and attention hybrid model to address these challenges. In addition to a first pre-training, a second pre-training stage allows us to specialise the model with high-quality data. We employ single nucleotide tokenization of mRNA sequences with codon separation, ensuring prior biological and structural information from the original mRNA sequence is not lost. Our model, Helix-mRNA, outperforms existing methods in analysing both UTRs and coding region properties. It can process sequences 6x longer than current approaches while using only 10% of the parameters of existing foundation models. Its predictive capabilities extend to all mRNA regions. We open-source the model (https://github.com/helicalAI/helical) and model weights (https://huggingface.co/helical-ai/helix-mRNA).

In this white paper we introduce Helix, an AI based solution for missense pathogenicity prediction. With recent advances in the sequencing of human genomes, massive amounts of genetic data have become available. This has shifted the burden of labor for genetic diagnostics and research from the gathering of data to its interpretation. Helix presents a state of the art platform for the prediction of pathogenicity in human missense variants. In addition to offering best-in-class predictive performance, Helix offers a platform that allows researchers to analyze and interpret variants in depth that can be accessed at helixlabs.ai.

Recovery of an underlying scene geometry from multiview images stands as a long-time challenge in computer vision research. The recent promise leverages neural implicit surface learning and differentiable volume rendering, and achieves both the recovery of scene geometry and synthesis of novel views, where deep priors of neural models are used as an inductive smoothness bias. While promising for object-level surfaces, these methods suffer when coping with complex scene surfaces. In the meanwhile, traditional multi-view stereo can recover the geometry of scenes with rich textures, by globally optimizing the local, pixel-wise correspondences across multiple views. We are thus motivated to make use of the complementary benefits from the two strategies, and propose a method termed Helix-shaped neural implicit Surface learning or HelixSurf; HelixSurf uses the intermediate prediction from one strategy as the guidance to regularize the learning of the other one, and conducts such intertwined regularization iteratively during the learning process. We also propose an efficient scheme for differentiable volume rendering in HelixSurf. Experiments on surface reconstruction of indoor scenes show that our method compares favorably with existing methods and is orders of magnitude faster, even when some of existing methods are assisted with auxiliary training data. The source code is available at https://github.com/Gorilla-Lab-SCUT/HelixSurf.

While current Multimodal Large Language Models (MLLMs) have demonstrated proficiency in reasoning tasks such as mathematics and logic, their capacity for long-chain reflective reasoning, a prerequisite for solving complex real-world problems, remains largely underexplored. In this work, we first conduct an extensive empirical investigation to evaluate this capability. Leveraging a carefully designed data synthesis engine, we construct MM-HELIX, a multimodal benchmark consisting 1,260 samples of 42 challenging synthetic tasks that require iterative thinking and backtracking. Empirical results on this benchmark reveal that existing MLLMs exhibit significant performance deficits in long-chain reflective reasoning. To address this limitation, we generate post-training data and further explore learning paradigms for exploiting such data. We first develop the Step-Elicited Response Generation pipeline to create MM-HELIX-100K, a large-scale dataset of 100k high-quality, reflective reasoning traces for instruction-tuning stage. Given that standard Reinforcement Learning fails on complex tasks due to sparse reward signals and catastrophic forgetting after Supervised Fine-Tuning, we propose Adaptive Hybrid Policy Optimization (AHPO), a novel training strategy that dynamically unifies offline supervision and online optimization into a single stage. This strategy enables the model to learn from expert data when rewards are sparse and conduct independent exploration once proficient. When applied to the Qwen2.5-VL-7B baseline, our method achieves a +18.6\% accuracy improvement on MM-HELIX benchmark and demonstrates strong generalization with a +5.7\% average performance gain on general mathematic and logic tasks. Our work demonstrate that reflective reasoning in MLLMs can be effectively learned and generalized, paving the way for developing more capable MLLMs.