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Publications
Multi-modal Molecule Structure-text Model for Text-based Retrieval and Editing
There is increasing adoption of artificial intelligence in drug discovery. However, existing studies use machine learning to mainly utilize … (voir plus)the chemical structures of molecules but ignore the vast textual knowledge available in chemistry. Incorporating textual knowledge enables us to realize new drug design objectives, adapt to text-based instructions and predict complex biological activities. Here we present a multi-modal molecule structure-text model, MoleculeSTM, by jointly learning molecules' chemical structures and textual descriptions via a contrastive learning strategy. To train MoleculeSTM, we construct a large multi-modal dataset, namely, PubChemSTM, with over 280,000 chemical structure-text pairs. To demonstrate the effectiveness and utility of MoleculeSTM, we design two challenging zero-shot tasks based on text instructions, including structure-text retrieval and molecule editing. MoleculeSTM has two main properties: open vocabulary and compositionality via natural language. In experiments, MoleculeSTM obtains the state-of-the-art generalization ability to novel biochemical concepts across various benchmarks.
Human diseases are characterized by intricate cellular dynamics. Single-cell sequencing provides critical insights, yet a persistent gap rem… (voir plus)ains in computational tools for detailed disease progression analysis and targeted in-silico drug interventions. Here, we introduce UNAGI, a deep generative neural network tailored to analyze time-series single-cell transcriptomic data. This tool captures the complex cellular dynamics underlying disease progression, enhancing drug perturbation modeling and discovery. When applied to a dataset from patients with Idiopathic Pulmonary Fibrosis (IPF), UNAGI learns disease-informed cell embeddings that sharpen our understanding of disease progression, leading to the identification of potential therapeutic drug candidates. Validation via proteomics reveals the accuracy of UNAGI’s cellular dynamics analyses, and the use of the Fibrotic Cocktail treated human Precision-cut Lung Slices confirms UNAGI’s predictions that Nifedipine, an antihypertensive drug, may have antifibrotic effects on human tissues. UNAGI’s versatility extends to other diseases, including a COVID dataset, demonstrating adaptability and confirming its broader applicability in decoding complex cellular dynamics beyond IPF, amplifying its utility in the quest for therapeutic solutions across diverse pathological landscapes.
Recent progress in self-supervised (SSL) visual representation learning has led to the development of several different proposed frameworks … (voir plus)that rely on augmentations of images but use different loss functions. However, there are few theoretically grounded principles to guide practice, so practical implementation of each SSL framework requires several heuristics to achieve competitive performance. In this work, we build on recent analytical results to design practical recommendations for competitive and efficient SSL that are grounded in theory. Specifically, recent theory tells us that existing SSL frameworks are minimizing the same idealized loss, which is to learn features that best match the data similarity kernel defined by the augmentations used. We show how this idealized loss can be reformulated to a functionally equivalent loss that is more efficient to compute. We study the implicit bias of using gradient descent to minimize our reformulated loss function and find that using a stronger orthogonalization constraint with a reduced projector dimensionality should yield good representations. Furthermore, the theory tells us that approximating the reformulated loss should be improved by increasing the number of augmentations, and as such using multiple augmentations should lead to improved convergence. We empirically verify our findings on CIFAR, STL and Imagenet datasets, wherein we demonstrate an improved linear readout performance when training a ResNet-backbone using our theoretically grounded recommendations. Remarkably, we also demonstrate that by leveraging these insights, we can reduce the pretraining dataset size by up to 2
Network design problems constitute an important family of combinatorial optimization problems for which numerous exact and heuristic algorit… (voir plus)hms have been developed over the last few decades. Two central problems in this family are the multi-commodity, capacitated, fixed charge network design problem (MCFNDP) and its stochastic counterpart, the two-stage MCFNDP with recourse. These are standard problems that often serve as work benches for devising and testing models and algorithms in stylized but close-to-realistic settings. The purpose of this paper is to introduce two flexible, high-speed generators capable of simulating a wide range of settings for both the deterministic and stochastic MCFNDPs. We hope that, by facilitating systematic experimentation with new and larger sets of instances, these generators will lead to a more thorough assessment of the performance achieved by exact and heuristic solution methods in both deterministic and stochastic settings. We also hope that making these generators available will promote the reproducibility and comparability of published research.
The BigCode community, an open-scientific collaboration working on the responsible development of Large Language Models for Code (Code LLMs)… (voir plus), introduces StarCoder and StarCoderBase: 15.5B parameter models with 8K context length, infilling capabilities and fast large-batch inference enabled by multi-query attention. StarCoderBase is trained on 1 trillion tokens sourced from The Stack, a large collection of permissively licensed GitHub repositories with inspection tools and an opt-out process. We fine-tuned StarCoderBase on 35B Python tokens, resulting in the creation of StarCoder. We perform the most comprehensive evaluation of Code LLMs to date and show that StarCoderBase outperforms every open Code LLM that supports multiple programming languages and matches or outperforms the OpenAI code-cushman-001 model. Furthermore, StarCoder outperforms every model that is fine-tuned on Python and still retains its performance on other programming languages. We take several important steps towards a safe open-access model release, including an improved PII redaction pipeline and a novel attribution tracing tool, and make the StarCoder models publicly available under a more commercially viable version of the Open Responsible AI Model license.
Scalable Vector Graphics (SVGs) are vital for modern image rendering due to their scalability and versatility. Previous SVG generation metho… (voir plus)ds have focused on curve-based vectorization, lacking semantic understanding, often producing artifacts, and struggling with SVG primitives beyond path curves. To address these issues, we introduce StarVector, a multimodal large language model for SVG generation. It performs image vectorization by understanding image semantics and using SVG primitives for compact, precise outputs. Unlike traditional methods, StarVector works directly in the SVG code space, leveraging visual understanding to apply accurate SVG primitives. To train StarVector, we create SVG-Stack, a diverse dataset of 2M samples that enables generalization across vectorization tasks and precise use of primitives like ellipses, polygons, and text. We address challenges in SVG evaluation, showing that pixel-based metrics like MSE fail to capture the unique qualities of vector graphics. We introduce SVG-Bench, a benchmark across 10 datasets, and 3 tasks: Image-to-SVG, Text-to-SVG generation, and diagram generation. Using this setup, StarVector achieves state-of-the-art performance, producing more compact and semantically rich SVGs.
Scalable Vector Graphics (SVGs) are vital for modern image rendering due to their scalability and versatility. Previous SVG generation metho… (voir plus)ds have focused on curve-based vectorization, lacking semantic understanding, often producing artifacts, and struggling with SVG primitives beyond path curves. To address these issues, we introduce StarVector, a multimodal large language model for SVG generation. It performs image vectorization by understanding image semantics and using SVG primitives for compact, precise outputs. Unlike traditional methods, StarVector works directly in the SVG code space, leveraging visual understanding to apply accurate SVG primitives. To train StarVector, we create SVG-Stack, a diverse dataset of 2M samples that enables generalization across vectorization tasks and precise use of primitives like ellipses, polygons, and text. We address challenges in SVG evaluation, showing that pixel-based metrics like MSE fail to capture the unique qualities of vector graphics. We introduce SVG-Bench, a benchmark across 10 datasets, and 3 tasks: Image-to-SVG, Text-to-SVG generation, and diagram generation. Using this setup, StarVector achieves state-of-the-art performance, producing more compact and semantically rich SVGs.
Scalable Vector Graphics (SVGs) have become integral in modern image rendering applications due to their infinite scalability in resolution,… (voir plus) versatile usability, and editing capabilities. SVGs are particularly popular in the fields of web development and graphic design. Existing approaches for SVG modeling using deep learning often struggle with generating complex SVGs and are restricted to simpler ones that require extensive processing and simplification. This paper introduces StarVector, a multimodal SVG generation model that effectively integrates Code Generation Large Language Models (CodeLLMs) and vision models. Our approach utilizes a CLIP image encoder to extract visual representations from pixel-based images, which are then transformed into visual tokens via an adapter module. These visual tokens are pre-pended to the SVG token embeddings, and the sequence is modeled by the StarCoder model using next-token prediction, effectively learning to align the visual and code tokens. This enables StarVector to generate unrestricted SVGs that accurately represent pixel images. To evaluate StarVector's performance, we present SVG-Bench, a comprehensive benchmark for evaluating SVG methods across multiple datasets and relevant metrics. Within this benchmark, we introduce novel datasets including SVG-Stack, a large-scale dataset of real-world SVG examples, and use it to pre-train StarVector as a large foundation model for SVGs. Our results demonstrate significant enhancements in visual quality and complexity handling over current methods, marking a notable advancement in SVG generation technology. Code and models: https://github.com/joanrod/star-vector
Despite the recent advancements in speech recognition, there are still difficulties in accurately transcribing conversational and emotional … (voir plus)speech in noisy and reverberant acoustic environments. This poses a particular challenge in the search and rescue (SAR) domain, where transcribing conversations among rescue team members is crucial to support real-time decision-making. The scarcity of speech data and associated background noise in SAR scenarios make it difficult to deploy robust speech recognition systems.To address this issue, we have created and made publicly available a German speech dataset called RescueSpeech. This dataset includes real speech recordings from simulated rescue exercises. Additionally, we have released competitive training recipes and pre-trained models. Our study highlights that the performance attained by state-of-the-art methods in this challenging scenario is still far from reaching an acceptable level.
2023-12-16
2023 IEEE Automatic Speech Recognition and Understanding Workshop (ASRU) (publié)
Speech Emotion Recognition (SER) typically relies on utterance-level solutions. However, emotions conveyed through speech should be consider… (voir plus)ed as discrete speech events with definite temporal boundaries, rather than attributes of the entire utterance. To reflect the fine-grained nature of speech emotions and to unify various fine-grained methods under a single objective, we propose a new task: Speech Emotion Diarization (SED). Just as Speaker Diarization answers the question of “Who speaks when?”, Speech Emotion Diarization answers the question of “Which emotion appears when?”. To facilitate the evaluation of the performance and establish a common benchmark, we introduce the Zaion Emotion Dataset (ZED), an openly accessible speech emotion dataset that includes non-acted emotions recorded in real-life conditions, along with manually annotated boundaries of emotion segments within the utterance. We provide competitive baselines and open-source the code and the pre-trained models.
2023-12-16
2023 IEEE Automatic Speech Recognition and Understanding Workshop (ASRU) (publié)
