Mass spectrometry plays a fundamental role in elucidating the structures of unknown molecules and subsequent scientific discoveries. One formulation of the structure elucidation task is the conditional de novo generation of molecular structure given a mass spectrum. Toward a more accurate and efficient scientific discovery pipeline for small molecules, we present DiffMS, a formula-restricted encoder-decoder generative network that achieves state-of-the-art performance on this task. The encoder utilizes a transformer architecture and models mass spectra domain knowledge such as peak formulae and neutral losses, and the decoder is a discrete graph diffusion model restricted by the heavy-atom composition of a known chemical formula. To develop a robust decoder that bridges latent embeddings and molecular structures, we pretrain the diffusion decoder with fingerprint-structure pairs, which are available in virtually infinite quantities, compared to structure-spectrum pairs that number in the tens of thousands. Extensive experiments on established benchmarks show that DiffMS outperforms existing models on de novo molecule generation. We provide several ablations to demonstrate the effectiveness of our diffusion and pretraining approaches and show consistent performance scaling with increasing pretraining dataset size. DiffMS code is publicly available at https://github.com/coleygroup/DiffMS.
Underwater dense prediction, especially depth estimation and semantic segmentation, is crucial for gaining a comprehensive understanding of underwater scenes. Nevertheless, high-quality and large-scale underwater datasets with dense annotations remain scarce because of the complex environment and the exorbitant data collection costs. This paper proposes a unified Text-to-Image and DEnse annotation generation method (TIDE) for underwater scenes. It relies solely on text as input to simultaneously generate realistic underwater images and multiple highly consistent dense annotations. Specifically, we unify the generation of text-to-image and text-to-dense annotations within a single model. The Implicit Layout Sharing mechanism (ILS) and cross-modal interaction method called Time Adaptive Normalization (TAN) are introduced to jointly optimize the consistency between image and dense annotations. We synthesize a large-scale underwater dataset using TIDE to validate the effectiveness of our method in underwater dense prediction tasks. The results demonstrate that our method effectively improves the performance of existing underwater dense prediction models and mitigates the scarcity of underwater data with dense annotations. We hope our method can offer new perspectives on alleviating data scarcity issues in other fields. The code is available at https: //github.com/HongkLin/TIDE.
Can we leverage LLMs to model the process of discovering novel language model (LM) architectures? Inspired by real research, we propose a multi-agent LLM approach that simulates the conventional stages of research, from ideation and literature search (proposal stage) to design implementation (code generation), generative pre-training, and downstream evaluation (verification). Using ideas from scaling laws, our system, Genesys, employs a Ladder of Scales approach; new designs are proposed, adversarially reviewed, implemented, and selectively verified at increasingly larger model scales (14M$\sim$350M parameters) with a narrowing budget (the number of models we can train at each scale). To help make discovery efficient and factorizable, Genesys uses a novel genetic programming backbone, which we show has empirical advantages over commonly used direct prompt generation workflows (e.g., $\sim$86\% percentage point improvement in successful design generation, a key bottleneck). We report experiments involving 1,162 newly discovered designs (1,062 fully verified through pre-training) and find the best designs to be highly competitive with known architectures (e.g., outperform GPT2, Mamba2, etc., on 6/9 common benchmarks). We couple these results with comprehensive system-level ablations and formal results, which give broader insights into the design of effective autonomous discovery systems.
Test-driven development (TDD) is the practice of writing tests first and coding later, and the proponents of TDD expound its numerous benefits. For instance, given an issue on a source code repository, tests can clarify the desired behavior among stake-holders before anyone writes code for the agreed-upon fix. Although there has been a lot of work on automated test generation for the practice "write code first, test later", there has been little such automation for TDD. Ideally, tests for TDD should be fail-to-pass (i.e., fail before the issue is resolved and pass after) and have good adequacy with respect to covering the code changed during issue resolution. This paper introduces TDD-Bench Verified, a high-quality benchmark suite of 449 issues mined from real-world GitHub code repositories. The benchmark's evaluation harness runs only relevant tests in isolation for simple yet accurate coverage measurements, and the benchmark's dataset is filtered both by human judges and by execution in the harness. This paper also presents Auto-TDD, an LLM-based solution that takes as input an issue description and a codebase (prior to issue resolution) and returns as output a test that can be used to validate the changes made for resolving the issue. Our evaluation shows that Auto-TDD yields a better fail-to-pass rate than the strongest prior work while also yielding high coverage adequacy. Overall, we hope that this work helps make developers more productive at resolving issues while simultaneously leading to more robust fixes.
Dialogue systems for non-English languages have long been under-explored. In this paper, we take the first step to investigate few-shot cross-lingual transfer learning (FS-XLT) and multitask learning (MTL) in the context of open-domain dialogue generation for non-English languages with limited data. We observed catastrophic forgetting in both FS-XLT and MTL for all 6 languages in our preliminary experiments. To mitigate the issue, we propose a simple yet effective prompt learning approach that can preserve the multilinguality of multilingual pre-trained language model (mPLM) in FS-XLT and MTL by bridging the gap between pre-training and fine-tuning with Fixed-prompt LM Tuning and our hand-crafted prompts. Experimental results on all 6 languages in terms of both automatic and human evaluations demonstrate the effectiveness of our approach. Our code is available at https://github.com/JeremyLeiLiu/XLinguDial.
Retrieving proper domain knowledge from an external database lies at the heart of end-to-end task-oriented dialog systems to generate informative responses. Most existing systems blend knowledge retrieval with response generation and optimize them with direct supervision from reference responses, leading to suboptimal retrieval performance when the knowledge base becomes large-scale. To address this, we propose to decouple knowledge retrieval from response generation and introduce a multi-grained knowledge retriever (MAKER) that includes an entity selector to search for relevant entities and an attribute selector to filter out irrelevant attributes. To train the retriever, we propose a novel distillation objective that derives supervision signals from the response generator. Experiments conducted on three standard benchmarks with both small and large-scale knowledge bases demonstrate that our retriever performs knowledge retrieval more effectively than existing methods. Our code has been made publicly available.\footnote{https://github.com/18907305772/MAKER}
To fully leverage the capabilities of diffusion models, we are often interested in optimizing downstream reward functions during inference. While numerous algorithms for reward-guided generation have been recently proposed due to their significance, current approaches predominantly focus on single-shot generation, transitioning from fully noised to denoised states. We propose a novel framework for inference-time reward optimization with diffusion models inspired by evolutionary algorithms. Our approach employs an iterative refinement process consisting of two steps in each iteration: noising and reward-guided denoising. This sequential refinement allows for the gradual correction of errors introduced during reward optimization. Besides, we provide a theoretical guarantee for our framework. Finally, we demonstrate its superior empirical performance in protein and cell-type-specific regulatory DNA design. The code is available at \href{https://github.com/masa-ue/ProDifEvo-Refinement}{https://github.com/masa-ue/ProDifEvo-Refinement}.
Large language models have been used to translate natural language questions to SQL queries. Without hard constraints on syntax and database schema, they occasionally produce invalid queries that are not executable. These failures limit the usage of these systems in real-life scenarios. We propose a neurosymbolic framework that imposes SQL syntax and schema constraints with unification-based definite clause grammars and thus guarantees the generation of valid queries. Our framework also builds a bi-directional interface to language models to leverage their natural language understanding abilities. The evaluation results on a subset of SQL grammars show that all our output queries are valid. This work is the first step towards extending language models with unification-based grammars. We demonstrate this extension enhances the validity, execution accuracy, and ground truth alignment of the underlying language model by a large margin. Our code is available at https://github.com/ML-KULeuven/deepstochlog-lm.
Uniform-state discrete diffusion models hold the promise of fast text generation due to their inherent ability to self-correct. However, they are typically outperformed by autoregressive models and masked diffusion models. In this work, we narrow this performance gap by leveraging a key insight: Uniform-state diffusion processes naturally emerge from an underlying Gaussian diffusion. Our method, Duo, transfers powerful techniques from Gaussian diffusion to improve both training and sampling. First, we introduce a curriculum learning strategy guided by the Gaussian process, doubling training speed by reducing variance. Models trained with curriculum learning surpass autoregressive models in zero-shot perplexity on 3 of 7 benchmarks. Second, we present Discrete Consistency Distillation, which adapts consistency distillation from the continuous to the discrete setting. This algorithm unlocks few-step generation in diffusion language models by accelerating sampling by two orders of magnitude. We provide the code and model checkpoints on the project page: http://s-sahoo.github.io/duo
In this work, we extend the SEEDS superpixel algorithm from 2D images to 3D volumes, resulting in 3D SEEDS, a faster, better, and open-source supervoxel algorithm for medical image analysis. We compare 3D SEEDS with the widely used supervoxel algorithm SLIC on 13 segmentation tasks across 10 organs. 3D SEEDS accelerates supervoxel generation by a factor of 10, improves the achievable Dice score by +6.5%, and reduces the under-segmentation error by -0.16%. The code is available at https://github.com/Zch0414/3d_seeds
Motivation: High-throughput sequencing of large immune repertoires has enabled the development of methods to predict the probability of generation by V(D)J recombination of T- and B-cell receptors of any specific nucleotide sequence. These generation probabilities are very non-homogeneous, ranging over 20 orders of magnitude in real repertoires. Since the function of a receptor really depends on its protein sequence, it is important to be able to predict this probability of generation at the amino acid level. However, brute-force summation over all the nucleotide sequences with the correct amino acid translation is computationally intractable. The purpose of this paper is to present a solution to this problem. Results: We use dynamic programming to construct an efficient and flexible algorithm, called OLGA (Optimized Likelihood estimate of immunoGlobulin Amino-acid sequences), for calculating the probability of generating a given CDR3 amino acid sequence or motif, with or without V/J restriction, as a result of V(D)J recombination in B or T cells. We apply it to databases of epitope-specific T-cell receptors to evaluate the probability that a typical human subject will possess T cells responsive to specific disease-associated epitopes. The model prediction shows an excellent agreement with published data. We suggest that OLGA may be a useful tool to guide vaccine design. Availability: Source code is available at https://github.com/zsethna/OLGA
Whistle contour extraction aims to derive animal whistles from time-frequency spectrograms as polylines. For toothed whales, whistle extraction results can serve as the basis for analyzing animal abundance, species identity, and social activities. During the last few decades, as long-term recording systems have become affordable, automated whistle extraction algorithms were proposed to process large volumes of recording data. Recently, a deep learning-based method demonstrated superior performance in extracting whistles under varying noise conditions. However, training such networks requires a large amount of labor-intensive annotation, which is not available for many species. To overcome this limitation, we present a framework of stage-wise generative adversarial networks (GANs), which compile new whistle data suitable for deep model training via three stages: generation of background noise in the spectrogram, generation of whistle contours, and generation of whistle signals. By separating the generation of different components in the samples, our framework composes visually promising whistle data and labels even when few expert annotated data are available. Regardless of the amount of human-annotated data, the proposed data augmentation framework leads to a consistent improvement in performance of the whistle extraction model, with a maximum increase of 1.69 in the whistle extraction mean F1-score. Our stage-wise GAN also surpasses one single GAN in improving whistle extraction models with augmented data. The data and code will be available at https://github.com/Paul-LiPu/CompositeGAN\_WhistleAugment.
Designing new molecules is essential for drug discovery and material science. Recently, deep generative models that aim to model molecule distribution have made promising progress in narrowing down the chemical research space and generating high-fidelity molecules. However, current generative models only focus on modeling either 2D bonding graphs or 3D geometries, which are two complementary descriptors for molecules. The lack of ability to jointly model both limits the improvement of generation quality and further downstream applications. In this paper, we propose a new joint 2D and 3D diffusion model (JODO) that generates complete molecules with atom types, formal charges, bond information, and 3D coordinates. To capture the correlation between molecular graphs and geometries in the diffusion process, we develop a Diffusion Graph Transformer to parameterize the data prediction model that recovers the original data from noisy data. The Diffusion Graph Transformer interacts node and edge representations based on our relational attention mechanism, while simultaneously propagating and updating scalar features and geometric vectors. Our model can also be extended for inverse molecular design targeting single or multiple quantum properties. In our comprehensive evaluation pipeline for unconditional joint generation, the results of the experiment show that JODO remarkably outperforms the baselines on the QM9 and GEOM-Drugs datasets. Furthermore, our model excels in few-step fast sampling, as well as in inverse molecule design and molecular graph generation. Our code is provided in https://github.com/GRAPH-0/JODO.
As demonstrated by GPT-3 and T5, transformers grow in capability as parameter spaces become larger and larger. However, for tasks that require a large amount of knowledge, non-parametric memory allows models to grow dramatically with a sub-linear increase in computational cost and GPU memory requirements. Recent models such as RAG and REALM have introduced retrieval into conditional generation. These models incorporate neural initial retrieval from a corpus of passages. We build on this line of research, proposing Re2G, which combines both neural initial retrieval and reranking into a BART-based sequence-to-sequence generation. Our reranking approach also permits merging retrieval results from sources with incomparable scores, enabling an ensemble of BM25 and neural initial retrieval. To train our system end-to-end, we introduce a novel variation of knowledge distillation to train the initial retrieval, reranker, and generation using only ground truth on the target sequence output. We find large gains in four diverse tasks: zero-shot slot filling, question answering, fact-checking, and dialog, with relative gains of 9% to 34% over the previous state-of-the-art on the KILT leaderboard. We make our code available as open source at https://github.com/IBM/kgi-slot-filling/tree/re2g.
Human-human communication is like a delicate dance where listeners and speakers concurrently interact to maintain conversational dynamics. Hence, an effective model for generating listener nonverbal behaviors requires understanding the dyadic context and interaction. In this paper, we present an effective framework for creating 3D facial motions in dyadic interactions. Existing work consider a listener as a reactive agent with reflexive behaviors to the speaker's voice and facial motions. The heart of our framework is Dyadic Interaction Modeling (DIM), a pre-training approach that jointly models speakers' and listeners' motions through masking and contrastive learning to learn representations that capture the dyadic context. To enable the generation of non-deterministic behaviors, we encode both listener and speaker motions into discrete latent representations, through VQ-VAE. The pre-trained model is further fine-tuned for motion generation. Extensive experiments demonstrate the superiority of our framework in generating listener motions, establishing a new state-of-the-art according to the quantitative measures capturing the diversity and realism of generated motions. Qualitative results demonstrate the superior capabilities of the proposed approach in generating diverse and realistic expressions, eye blinks and head gestures. The code is available at https://github.com/Boese0601/Dyadic-Interaction-Modeling
Generative models aim to simulate realistic effects of various actions across different contexts, from text generation to visual effects. Despite significant efforts to build real-world simulators, the application of generative models to virtual worlds, like financial markets, remains under-explored. In financial markets, generative models can simulate complex market effects of participants with various behaviors, enabling interaction under different market conditions, and training strategies without financial risk. This simulation relies on the finest structured data in financial market like orders thus building the finest realistic simulation. We propose Large Market Model (LMM), an order-level generative foundation model, for financial market simulation, akin to language modeling in the digital world. Our financial Market Simulation engine (MarS), powered by LMM, addresses the domain-specific need for realistic, interactive and controllable order generation. Key observations include LMM's strong scalability across data size and model complexity, and MarS's robust and practicable realism in controlled generation with market impact. We showcase MarS as a forecast tool, detection system, analysis platform, and agent training environment, thus demonstrating MarS's "paradigm shift" potential for a variety of financial applications. We release the code of MarS at https://github.com/microsoft/MarS/.
Simulation-based testing has emerged as an essential tool for verifying and validating autonomous vehicles (AVs). However, contemporary methodologies, such as deterministic and imitation learning-based driver models, struggle to capture the variability of human-like driving behavior. Given these challenges, we propose HAD-Gen, a general framework for realistic traffic scenario generation that simulates diverse human-like driving behaviors. The framework first clusters the vehicle trajectory data into different driving styles according to safety features. It then employs maximum entropy inverse reinforcement learning on each of the clusters to learn the reward function corresponding to each driving style. Using these reward functions, the method integrates offline reinforcement learning pre-training and multi-agent reinforcement learning algorithms to obtain general and robust driving policies. Multi-perspective simulation results show that our proposed scenario generation framework can simulate diverse, human-like driving behaviors with strong generalization capability. The proposed framework achieves a 90.96% goal-reaching rate, an off-road rate of 2.08%, and a collision rate of 6.91% in the generalization test, outperforming prior approaches by over 20% in goal-reaching performance. The source code is released at https://github.com/RoboSafe-Lab/Sim4AD.
The progress on generative models has led to significant advances on text-to-video (T2V) generation, yet the motion controllability of generated videos remains limited. Existing motion transfer methods explored the motion representations of reference videos to guide generation. Nevertheless, these methods typically rely on sample-specific optimization strategy, resulting in high computational burdens. In this paper, we propose EfficientMT, a novel and efficient end-to-end framework for video motion transfer. By leveraging a small set of synthetic paired motion transfer samples, EfficientMT effectively adapts a pretrained T2V model into a general motion transfer framework that can accurately capture and reproduce diverse motion patterns. Specifically, we repurpose the backbone of the T2V model to extract temporal information from reference videos, and further propose a scaler module to distill motion-related information. Subsequently, we introduce a temporal integration mechanism that seamlessly incorporates reference motion features into the video generation process. After training on our self-collected synthetic paired samples, EfficientMT enables general video motion transfer without requiring test-time optimization. Extensive experiments demonstrate that our EfficientMT outperforms existing methods in efficiency while maintaining flexible motion controllability. Our code will be available https://github.com/PrototypeNx/EfficientMT.
We present UniTEX, a novel two-stage 3D texture generation framework to create high-quality, consistent textures for 3D assets. Existing approaches predominantly rely on UV-based inpainting to refine textures after reprojecting the generated multi-view images onto the 3D shapes, which introduces challenges related to topological ambiguity. To address this, we propose to bypass the limitations of UV mapping by operating directly in a unified 3D functional space. Specifically, we first propose that lifts texture generation into 3D space via Texture Functions (TFs)--a continuous, volumetric representation that maps any 3D point to a texture value based solely on surface proximity, independent of mesh topology. Then, we propose to predict these TFs directly from images and geometry inputs using a transformer-based Large Texturing Model (LTM). To further enhance texture quality and leverage powerful 2D priors, we develop an advanced LoRA-based strategy for efficiently adapting large-scale Diffusion Transformers (DiTs) for high-quality multi-view texture synthesis as our first stage. Extensive experiments demonstrate that UniTEX achieves superior visual quality and texture integrity compared to existing approaches, offering a generalizable and scalable solution for automated 3D texture generation. Code will available in: https://github.com/YixunLiang/UniTEX.
Automating radiology report generation can ease the reporting workload for radiologists. However, existing works focus mainly on the chest area due to the limited availability of public datasets for other regions. Besides, they often rely on naive data-driven approaches, e.g., a basic encoder-decoder framework with captioning loss, which limits their ability to recognise complex patterns across diverse anatomical regions. To address these issues, we propose X-RGen, a radiologist-minded report generation framework across six anatomical regions. In X-RGen, we seek to mimic the behaviour of human radiologists, breaking them down into four principal phases: 1) initial observation, 2) cross-region analysis, 3) medical interpretation, and 4) report formation. Firstly, we adopt an image encoder for feature extraction, akin to a radiologist's preliminary review. Secondly, we enhance the recognition capacity of the image encoder by analysing images and reports across various regions, mimicking how radiologists gain their experience and improve their professional ability from past cases. Thirdly, just as radiologists apply their expertise to interpret radiology images, we introduce radiological knowledge of multiple anatomical regions to further analyse the features from a clinical perspective. Lastly, we generate reports based on the medical-aware features using a typical auto-regressive text decoder. Both natural language generation (NLG) and clinical efficacy metrics show the effectiveness of X-RGen on six X-ray datasets. Our code and checkpoints are available at: https://github.com/YtongXie/X-RGen.