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.

Active Galactic Nuclei (AGN) are some of the most luminous and extreme environments in the Universe. The central engines of AGN, believed to be super-massive black-holes, are fed by accretion discs threaded by magnetic fields within a dense magneto-ionic medium. We report our findings from polarimetric Very-long-baseline Interferometry (VLBI) observations of quasar NRAO150 taken in October 2022 using a combined network of the Very Long Baseline Array (VLBA) and Effelsberg 100-m Radio Telescope. These observations are the first co-temporal multi-frequency polarimetric VLBI observations of NRAO150 at frequencies above 15GHz. We use the new VLBI polarization calibration procedure, GPCAL, with polarization observations of frequencies of 12GHz, 15GHz, 24GHz, and 43GHz of NRAO150. From these observations, we measure Faraday rotation. Using our measurement of Faraday rotation, we also derive the intrinsic electric vector position angle (EVPA0) for the source. As a complementary measurement we determine the behavior of polarization as a function of observed frequency. The polarization from NRAO150 only comes from the core region, with a peak polarization intensity occurring at 24GHz. Across the core region of NRAO150 we see clear gradients in Faraday rotation and EVPA0 values that are aligned with the direction of the jet curving around the core region. We find that for the majority of the polarized region the polarization fraction is greater at higher frequencies, with intrinsic polarization fractions in the core 3%. The Faraday rotation gradients and circular patterns in EVPA0 are strong evidence for a helical/toroidal magnetic field, and the presence of low intrinsic polarization fractions indicate that the polarized emission and hence the helical/toroidal magnetic field, occur within the innermost jet.

Deep learning-based methods have been widely researched in the areas of language and vision, demonstrating their capacity to understand long sequences of data and their usefulness in numerous helio-physics applications. Foundation models (FMs), which are pre-trained on a large-scale datasets, form the basis for a variety of downstream tasks. These models, especially those based on transformers in vision and language, show exceptional potential for adapting to a wide range of downstream applications. In this paper, we provide our perspective on the criteria for designing an FM for heliophysics and associated challenges and applications using the Solar Dynamics Observatory (SDO) dataset. We believe that this is the first study to design an FM in the domain of heliophysics.

TOI-836 is a ~2-3 Gyr K dwarf with an inner super Earth (R=1.7 R_oplus, P=3.8 d) and an outer mini Neptune (R=2.6 R_oplus, P=8.6 d). JWST/NIRSpec 2.8--5.2 mum transmission spectra are flat for both planets. We present Keck/NIRSPEC observations of escaping helium for super-Earth b, which shows no excess absorption in the 1083 nm triplet to deep limits (<0.2%), and mini-Neptune c, which shows strong (0.7%) excess absorption in both visits. These results demonstrate that planet c retains at least some primordial atmosphere, while planet b is consistent with having lost its entire primordial envelope. Self-consistent 1D radiative-hydrodynamic models of planet c reveal that the helium excess absorption signal is highly sensitive to metallicity: its equivalent width collapses by a factor of 13 as metallicity increases from 10x to 100x solar, and by a further factor of 12 as it increases to 200x solar. The observed equivalent width is 88\% the model prediction for 100x metallicity, suggesting an atmospheric metallicity similar to K2-18b and TOI-270d, the first two mini-Neptunes with detected absorption features in JWST transmission spectra. We highlight the helium triplet as a potentially powerful probe of atmospheric composition, with complementary strengths and weaknesses to atmospheric retrievals. The main strength is its extreme sensitivity to metallicity in the scientifically significant range of 10--200x solar, and the main weakness is the enormous model uncertainties in outflow suppression and confinement mechanisms, such as magnetic fields and stellar winds, which can suppress the signal by at least a factor of ~several.

Switchbacks are discrete angular deflections in the solar wind magnetic field that have been observed throughout the heliosphere. Recent observations by Parker Solar Probe (PSP) have revealed the presence of patches of switchbacks on the scale of hours to days, separated by 'quieter' radial fields. We aim to further diagnose the origin of these patches using measurements of proton temperature anisotropy that can illuminate possible links to formation processes in the solar corona. We fitted 3D bi-Maxwellian functions to the core of proton velocity distributions measured by the SPAN-Ai instrument onboard PSP to obtain the proton parallel, T_{p,|}, and perpendicular, T_{p,perp}, temperature. We show that the presence of patches is highlighted by a transverse deflection in the flow and magnetic field away from the radial direction. These deflections are correlated with enhancements in T_{p,|}, while T_{p,perp} remains relatively constant. Patches sometimes exhibit small proton and electron density enhancements. We interpret that patches are not simply a group of switchbacks, but rather switchbacks are embedded within a larger-scale structure identified by enhanced T_{p,|} that is distinct from the surrounding solar wind. We suggest that these observations are consistent with formation by reconnection-associated mechanisms in the corona.

Gaussian analysis of new, high-angular-resolution interstellar 21-cm neutral hydrogen emission profile structure more clearly reveals the presence of the previously reported signature of the critical ionization velocity ({\it CIV}) of Helium (34 km s^{-1}). The present analysis includes 1496 component line widths for 178 neutral hydrogen profiles in two areas of sky at galactic latitudes around -50^circ, well away from the galactic plane. The new data considered here allow the interstellar abundance of Helium to be calculated, and the derived value of 0.095 pm 0.020 compares extremely well with the value of 0.085 for the cosmic abundance based on solar data. Although the precise mechanisms that give rise to the {\it CIV} effect in interstellar space are not yet understood, our results may provide additional motivation for further theoretical study of how the mechanism operates.

In this paper, we introduce SoloAudio, a novel diffusion-based generative model for target sound extraction (TSE). Our approach trains latent diffusion models on audio, replacing the previous U-Net backbone with a skip-connected Transformer that operates on latent features. SoloAudio supports both audio-oriented and language-oriented TSE by utilizing a CLAP model as the feature extractor for target sounds. Furthermore, SoloAudio leverages synthetic audio generated by state-of-the-art text-to-audio models for training, demonstrating strong generalization to out-of-domain data and unseen sound events. We evaluate this approach on the FSD Kaggle 2018 mixture dataset and real data from AudioSet, where SoloAudio achieves the state-of-the-art results on both in-domain and out-of-domain data, and exhibits impressive zero-shot and few-shot capabilities. Source code and demos are released.

Recent advancements in generative artificial intelligence have significantly transformed the field of style-captioned text-to-speech synthesis (CapTTS). However, adapting CapTTS to real-world applications remains challenging due to the lack of standardized, comprehensive datasets and limited research on downstream tasks built upon CapTTS. To address these gaps, we introduce CapSpeech, a new benchmark designed for a series of CapTTS-related tasks, including style-captioned text-to-speech synthesis with sound events (CapTTS-SE), accent-captioned TTS (AccCapTTS), emotion-captioned TTS (EmoCapTTS), and text-to-speech synthesis for chat agent (AgentTTS). CapSpeech comprises over 10 million machine-annotated audio-caption pairs and nearly 0.36 million human-annotated audio-caption pairs. In addition, we introduce two new datasets collected and recorded by a professional voice actor and experienced audio engineers, specifically for the AgentTTS and CapTTS-SE tasks. Alongside the datasets, we conduct comprehensive experiments using both autoregressive and non-autoregressive models on CapSpeech. Our results demonstrate high-fidelity and highly intelligible speech synthesis across a diverse range of speaking styles. To the best of our knowledge, CapSpeech is the largest available dataset offering comprehensive annotations for CapTTS-related tasks. The experiments and findings further provide valuable insights into the challenges of developing CapTTS systems.

Taming the generation outcome of state of the art Diffusion and Flow-Matching (FM) models without having to re-train a task-specific model unlocks a powerful tool for solving inverse problems, conditional generation, and controlled generation in general. In this work we introduce D-Flow, a simple framework for controlling the generation process by differentiating through the flow, optimizing for the source (noise) point. We motivate this framework by our key observation stating that for Diffusion/FM models trained with Gaussian probability paths, differentiating through the generation process projects gradient on the data manifold, implicitly injecting the prior into the optimization process. We validate our framework on linear and non-linear controlled generation problems including: image and audio inverse problems and conditional molecule generation reaching state of the art performance across all.

Target Speech Extraction (TSE) aims to isolate a target speaker's voice from a mixture of multiple speakers by leveraging speaker-specific cues, typically provided as auxiliary audio (a.k.a. cue audio). Although recent advancements in TSE have primarily employed discriminative models that offer high perceptual quality, these models often introduce unwanted artifacts, reduce naturalness, and are sensitive to discrepancies between training and testing environments. On the other hand, generative models for TSE lag in perceptual quality and intelligibility. To address these challenges, we present SoloSpeech, a novel cascaded generative pipeline that integrates compression, extraction, reconstruction, and correction processes. SoloSpeech features a speaker-embedding-free target extractor that utilizes conditional information from the cue audio's latent space, aligning it with the mixture audio's latent space to prevent mismatches. Evaluated on the widely-used Libri2Mix dataset, SoloSpeech achieves the new state-of-the-art intelligibility and quality in target speech extraction and speech separation tasks while demonstrating exceptional generalization on out-of-domain data and real-world scenarios.

In this paper, we introduce SSR-Speech, a neural codec autoregressive model designed for stable, safe, and robust zero-shot text-based speech editing and text-to-speech synthesis. SSR-Speech is built on a Transformer decoder and incorporates classifier-free guidance to enhance the stability of the generation process. A watermark Encodec is proposed to embed frame-level watermarks into the edited regions of the speech so that which parts were edited can be detected. In addition, the waveform reconstruction leverages the original unedited speech segments, providing superior recovery compared to the Encodec model. Our approach achieves the state-of-the-art performance in the RealEdit speech editing task and the LibriTTS text-to-speech task, surpassing previous methods. Furthermore, SSR-Speech excels in multi-span speech editing and also demonstrates remarkable robustness to background sounds. Source code and demos are released.

Image manipulation can be considered a special case of image generation where the image to be produced is a modification of an existing image. Image generation and manipulation have been, for the most part, tasks that operate on raw pixels. However, the remarkable progress in learning rich image and object representations has opened the way for tasks such as text-to-image or layout-to-image generation that are mainly driven by semantics. In our work, we address the novel problem of image manipulation from scene graphs, in which a user can edit images by merely applying changes in the nodes or edges of a semantic graph that is generated from the image. Our goal is to encode image information in a given constellation and from there on generate new constellations, such as replacing objects or even changing relationships between objects, while respecting the semantics and style from the original image. We introduce a spatio-semantic scene graph network that does not require direct supervision for constellation changes or image edits. This makes it possible to train the system from existing real-world datasets with no additional annotation effort.

Perception systems play a crucial role in autonomous driving, incorporating multiple sensors and corresponding computer vision algorithms. 3D LiDAR sensors are widely used to capture sparse point clouds of the vehicle's surroundings. However, such systems struggle to perceive occluded areas and gaps in the scene due to the sparsity of these point clouds and their lack of semantics. To address these challenges, Semantic Scene Completion (SSC) jointly predicts unobserved geometry and semantics in the scene given raw LiDAR measurements, aiming for a more complete scene representation. Building on promising results of diffusion models in image generation and super-resolution tasks, we propose their extension to SSC by implementing the noising and denoising diffusion processes in the point and semantic spaces individually. To control the generation, we employ semantic LiDAR point clouds as conditional input and design local and global regularization losses to stabilize the denoising process. We evaluate our approach on autonomous driving datasets and our approach outperforms the state-of-the-art for SSC.

Speech separation, the task of isolating multiple speech sources from a mixed audio signal, remains challenging in noisy environments. In this paper, we propose a generative correction method to enhance the output of a discriminative separator. By leveraging a generative corrector based on a diffusion model, we refine the separation process for single-channel mixture speech by removing noises and perceptually unnatural distortions. Furthermore, we optimize the generative model using a predictive loss to streamline the diffusion model's reverse process into a single step and rectify any associated errors by the reverse process. Our method achieves state-of-the-art performance on the in-domain Libri2Mix noisy dataset, and out-of-domain WSJ with a variety of noises, improving SI-SNR by 22-35% relative to SepFormer, demonstrating robustness and strong generalization capabilities.

3D head animation has seen major quality and runtime improvements over the last few years, particularly empowered by the advances in differentiable rendering and neural radiance fields. Real-time rendering is a highly desirable goal for real-world applications. We propose HeadGaS, a model that uses 3D Gaussian Splats (3DGS) for 3D head reconstruction and animation. In this paper we introduce a hybrid model that extends the explicit 3DGS representation with a base of learnable latent features, which can be linearly blended with low-dimensional parameters from parametric head models to obtain expression-dependent color and opacity values. We demonstrate that HeadGaS delivers state-of-the-art results in real-time inference frame rates, surpassing baselines by up to 2dB, while accelerating rendering speed by over x10.