Daily Papers

Recent advances in molecular foundation models have shown impressive performance in molecular property prediction and de novo molecular design, with promising applications in areas such as drug discovery and reaction prediction. Nevertheless, most existing approaches rely exclusively on SMILES representations and overlook both experimental spectra and 3D structural information-two indispensable sources for capturing molecular behavior in real-world scenarios. This limitation reduces their effectiveness in tasks where stereochemistry, spatial conformation, and experimental validation are critical. To overcome these challenges, we propose MolSpectLLM, a molecular foundation model pretrained on Qwen2.5-7B that unifies experimental spectroscopy with molecular 3D structure. By explicitly modeling molecular spectra, MolSpectLLM achieves state-of-the-art performance on spectrum-related tasks, with an average accuracy of 0.53 across NMR, IR, and MS benchmarks. MolSpectLLM also shows strong performance on the spectra analysis task, obtaining 15.5% sequence accuracy and 41.7% token accuracy on Spectra-to-SMILES, substantially outperforming large general-purpose LLMs. More importantly, MolSpectLLM not only achieves strong performance on molecular elucidation tasks, but also generates accurate 3D molecular structures directly from SMILES or spectral inputs, bridging spectral analysis, molecular elucidation, and molecular design. Code are available at https://github.com/Eurekashen/MolSpectLLM{https://github.com/Eurekashen/MolSpectLLM}.

Molecular structure elucidation from spectra is a foundational problem in chemistry, with profound implications for compound identification, synthesis, and drug development. Traditional methods rely heavily on expert interpretation and lack scalability. Pioneering machine learning methods have introduced retrieval-based strategies, but their reliance on finite libraries limits generalization to novel molecules. Generative models offer a promising alternative, yet most adopt autoregressive SMILES-based architectures that overlook 3D geometry and struggle to integrate diverse spectral modalities. In this work, we present DiffSpectra, a generative framework that directly infers both 2D and 3D molecular structures from multi-modal spectral data using diffusion models. DiffSpectra formulates structure elucidation as a conditional generation process. Its denoising network is parameterized by Diffusion Molecule Transformer, an SE(3)-equivariant architecture that integrates topological and geometric information. Conditioning is provided by SpecFormer, a transformer-based spectral encoder that captures intra- and inter-spectral dependencies from multi-modal spectra. Extensive experiments demonstrate that DiffSpectra achieves high accuracy in structure elucidation, recovering exact structures with 16.01% top-1 accuracy and 96.86% top-20 accuracy through sampling. The model benefits significantly from 3D geometric modeling, SpecFormer pre-training, and multi-modal conditioning. These results highlight the effectiveness of spectrum-conditioned diffusion modeling in addressing the challenge of molecular structure elucidation. To our knowledge, DiffSpectra is the first framework to unify multi-modal spectral reasoning and joint 2D/3D generative modeling for de novo molecular structure elucidation.

Image captioning aims to describe visual content in natural language. As 'a picture is worth a thousand words', there could be various correct descriptions for an image. However, with maximum likelihood estimation as the training objective, the captioning model is penalized whenever its prediction mismatches with the label. For instance, when the model predicts a word expressing richer semantics than the label, it will be penalized and optimized to prefer more concise expressions, referred to as conciseness optimization. In contrast, predictions that are more concise than labels lead to richness optimization. Such conflicting optimization directions could eventually result in the model generating general descriptions. In this work, we introduce Semipermeable MaxImum Likelihood Estimation (SMILE), which allows richness optimization while blocking conciseness optimization, thus encouraging the model to generate longer captions with more details. Extensive experiments on two mainstream image captioning datasets MSCOCO and Flickr30K demonstrate that SMILE significantly enhances the descriptiveness of generated captions. We further provide in-depth investigations to facilitate a better understanding of how SMILE works.

Masked video modeling, such as VideoMAE, is an effective paradigm for video self-supervised learning (SSL). However, they are primarily based on reconstructing pixel-level details on natural videos which have substantial temporal redundancy, limiting their capability for semantic representation and sufficient encoding of motion dynamics. To address these issues, this paper introduces a novel SSL approach for video representation learning, dubbed as SMILE, by infusing both spatial and motion semantics. In SMILE, we leverage image-language pretrained models, such as CLIP, to guide the learning process with their high-level spatial semantics. We enhance the representation of motion by introducing synthetic motion patterns in the training data, allowing the model to capture more complex and dynamic content. Furthermore, using SMILE, we establish a new self-supervised video learning paradigm capable of learning strong video representations without requiring any natural video data. We have carried out extensive experiments on 7 datasets with various downstream scenarios. SMILE surpasses current state-of-the-art SSL methods, showcasing its effectiveness in learning more discriminative and generalizable video representations. Code is available: https://github.com/fmthoker/SMILE

There will be a paradigm shift in chemical and biological research, to be enabled by autonomous, closed-loop, real-time self-directed decision-making experimentation. Spectrum-to-structure correlation, which is to elucidate molecular structures with spectral information, is the core step in understanding the experimental results and to close the loop. However, current approaches usually divide the task into either database-dependent retrieval and database-independent generation and neglect the inherent complementarity between them. In this study, we proposed Vib2Mol, a general deep learning model designed to flexibly handle diverse spectrum-to-structure tasks according to the available prior knowledge by bridging the retrieval and generation. It achieves state-of-the-art performance, even for the most demanding Raman spectra, over previous models in predicting reaction products and sequencing peptides as well as analyzing experimental spectra and integrating multi-modal spectral data. Vib2Mol enables vibrational spectroscopy a real-time guide for autonomous scientific discovery workflows.

Large language models (LLMs) are increasingly recognized as powerful tools for scientific discovery, particularly in molecular science. A fundamental requirement for these models is the ability to accurately understand molecular structures, commonly encoded in the SMILES representation. However, current LLMs struggle to interpret SMILES, even failing to carry out basic tasks such as counting molecular rings. To address this limitation, we introduce CLEANMOL, a novel framework that formulates SMILES parsing into a suite of clean and deterministic tasks explicitly designed to promote graph-level molecular comprehension. These tasks span from subgraph matching to global graph matching, providing structured supervision aligned with molecular structural properties. We construct a molecular pretraining dataset with adaptive difficulty scoring and pre-train open-source LLMs on these tasks. Our results show that CLEANMOL not only enhances structural comprehension but also achieves the best or competes with the baseline on the Mol-Instructions benchmark.

Existing visual parsers for molecule diagrams translate pixel-based raster images such as PNGs to chemical structure representations (e.g., SMILES). However, PDFs created by word processors including LaTeX and Word provide explicit locations and shapes for characters, lines, and polygons. We extract symbols from born-digital PDF molecule images and then apply simple graph transformations to capture both visual and chemical structure in editable ChemDraw files (CDXML). Our fast ( PDF rightarrow visual graph rightarrow chemical graph ) pipeline does not require GPUs, Optical Character Recognition (OCR) or vectorization. We evaluate on standard benchmarks using SMILES strings, along with a novel evaluation that provides graph-based metrics and error compilation using LgEval. The geometric information in born-digital PDFs produces a highly accurate parser, motivating generating training data for visual parsers that recognize from raster images, with extracted graphics, visual structure, and chemical structure as annotations. To do this we render SMILES strings in Indigo, parse molecule structure, and then validate recognized structure to select correct files.

Compound identification and structure annotation from mass spectra is a well-established task widely applied in drug detection, criminal forensics, small molecule biomarker discovery and chemical engineering. We propose SpecTUS: Spectral Translator for Unknown Structures, a deep neural model that addresses the task of structural annotation of small molecules from low-resolution gas chromatography electron ionization mass spectra (GC-EI-MS). Our model analyzes the spectra in de novo manner -- a direct translation from the spectra into 2D-structural representation. Our approach is particularly useful for analyzing compounds unavailable in spectral libraries. In a rigorous evaluation of our model on the novel structure annotation task across different libraries, we outperformed standard database search techniques by a wide margin. On a held-out testing set, including 28267 spectra from the NIST database, we show that our model's single suggestion perfectly reconstructs 43\% of the subset's compounds. This single suggestion is strictly better than the candidate of the database hybrid search (common method among practitioners) in 76\% of cases. In a~still affordable scenario of~10 suggestions, perfect reconstruction is achieved in 65\%, and 84\% are better than the hybrid search.

Language models demonstrate fundamental abilities in syntax, semantics, and reasoning, though their performance often depends significantly on the inputs they process. This study introduces TSIS (Simplified TSID) and its variants:TSISD (TSIS with Depth-First Search), TSISO (TSIS in Order), and TSISR (TSIS in Random), as integral components of the t-SMILES framework. These additions complete the framework's design, providing diverse approaches to molecular representation. Through comprehensive analysis and experiments employing deep generative models, including GPT, diffusion models, and reinforcement learning, the findings reveal that the hierarchical structure of t-SMILES is more straightforward to parse than initially anticipated. Furthermore, t-SMILES consistently outperforms other linear representations such as SMILES, SELFIES, and SAFE, demonstrating superior convergence speed and enhanced generalization capabilities.

Laughter is one of the most expressive and natural aspects of human speech, conveying emotions, social cues, and humor. However, most text-to-speech (TTS) systems lack the ability to produce realistic and appropriate laughter sounds, limiting their applications and user experience. While there have been prior works to generate natural laughter, they fell short in terms of controlling the timing and variety of the laughter to be generated. In this work, we propose ELaTE, a zero-shot TTS that can generate natural laughing speech of any speaker based on a short audio prompt with precise control of laughter timing and expression. Specifically, ELaTE works on the audio prompt to mimic the voice characteristic, the text prompt to indicate the contents of the generated speech, and the input to control the laughter expression, which can be either the start and end times of laughter, or the additional audio prompt that contains laughter to be mimicked. We develop our model based on the foundation of conditional flow-matching-based zero-shot TTS, and fine-tune it with frame-level representation from a laughter detector as additional conditioning. With a simple scheme to mix small-scale laughter-conditioned data with large-scale pre-training data, we demonstrate that a pre-trained zero-shot TTS model can be readily fine-tuned to generate natural laughter with precise controllability, without losing any quality of the pre-trained zero-shot TTS model. Through the evaluations, we show that ELaTE can generate laughing speech with significantly higher quality and controllability compared to conventional models. See https://aka.ms/elate/ for demo samples.

Establishing the relationship between 3D structures and the energy states of molecular systems has proven to be a promising approach for learning 3D molecular representations. However, existing methods are limited to modeling the molecular energy states from classical mechanics. This limitation results in a significant oversight of quantum mechanical effects, such as quantized (discrete) energy level structures, which offer a more accurate estimation of molecular energy and can be experimentally measured through energy spectra. In this paper, we propose to utilize the energy spectra to enhance the pre-training of 3D molecular representations (MolSpectra), thereby infusing the knowledge of quantum mechanics into the molecular representations. Specifically, we propose SpecFormer, a multi-spectrum encoder for encoding molecular spectra via masked patch reconstruction. By further aligning outputs from the 3D encoder and spectrum encoder using a contrastive objective, we enhance the 3D encoder's understanding of molecules. Evaluations on public benchmarks reveal that our pre-trained representations surpass existing methods in predicting molecular properties and modeling dynamics.

Knowledge of mixtures' phase equilibria is crucial in nature and technical chemistry. Phase equilibria calculations of mixtures require activity coefficients. However, experimental data on activity coefficients is often limited due to high cost of experiments. For an accurate and efficient prediction of activity coefficients, machine learning approaches have been recently developed. However, current machine learning approaches still extrapolate poorly for activity coefficients of unknown molecules. In this work, we introduce the SMILES-to-Properties-Transformer (SPT), a natural language processing network to predict binary limiting activity coefficients from SMILES codes. To overcome the limitations of available experimental data, we initially train our network on a large dataset of synthetic data sampled from COSMO-RS (10 Million data points) and then fine-tune the model on experimental data (20 870 data points). This training strategy enables SPT to accurately predict limiting activity coefficients even for unknown molecules, cutting the mean prediction error in half compared to state-of-the-art models for activity coefficient predictions such as COSMO-RS, UNIFAC, and improving on recent machine learning approaches.

Sarcastic speech synthesis, which involves generating speech that effectively conveys sarcasm, is essential for enhancing natural interactions in applications such as entertainment and human-computer interaction. However, synthesizing sarcastic speech remains a challenge due to the nuanced prosody that characterizes sarcasm, as well as the limited availability of annotated sarcastic speech data. To address these challenges, this study introduces a novel approach that integrates feedback loss from a bi-modal sarcasm detection model into the TTS training process, enhancing the model's ability to capture and convey sarcasm. In addition, by leveraging transfer learning, a speech synthesis model pre-trained on read speech undergoes a two-stage fine-tuning process. First, it is fine-tuned on a diverse dataset encompassing various speech styles, including sarcastic speech. In the second stage, the model is further refined using a dataset focused specifically on sarcastic speech, enhancing its ability to generate sarcasm-aware speech. Objective and subjective evaluations demonstrate that our proposed methods improve the quality, naturalness, and sarcasm-awareness of synthesized speech.

Laughter is a unique expression, essential to affirmative social interactions of humans. Although current 3D talking head generation methods produce convincing verbal articulations, they often fail to capture the vitality and subtleties of laughter and smiles despite their importance in social context. In this paper, we introduce a novel task to generate 3D talking heads capable of both articulate speech and authentic laughter. Our newly curated dataset comprises 2D laughing videos paired with pseudo-annotated and human-validated 3D FLAME parameters and vertices. Given our proposed dataset, we present a strong baseline with a two-stage training scheme: the model first learns to talk and then acquires the ability to express laughter. Extensive experiments demonstrate that our method performs favorably compared to existing approaches in both talking head generation and expressing laughter signals. We further explore potential applications on top of our proposed method for rigging realistic avatars.