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SubscribeAutomatically Extracting Web API Specifications from HTML Documentation
Web API specifications are machine-readable descriptions of APIs. These specifications, in combination with related tooling, simplify and support the consumption of APIs. However, despite the increased distribution of web APIs, specifications are rare and their creation and maintenance heavily relies on manual efforts by third parties. In this paper, we propose an automatic approach and an associated tool called D2Spec for extracting specifications from web API documentation pages. Given a seed online documentation page on an API, D2Spec first crawls all documentation pages on the API, and then uses a set of machine learning techniques to extract the base URL, path templates, and HTTP methods, which collectively describe the endpoints of an API. We evaluated whether D2Spec can accurately extract endpoints from documentation on 120 web APIs. The results showed that D2Spec achieved a precision of 87.5% in identifying base URLs, a precision of 81.3% and a recall of 80.6% in generating path templates, and a precision of 84.4% and a recall of 76.2% in extracting HTTP methods. In addition, we found that D2Spec was useful when applied to APIs with pre-existing API specifications: D2Spec revealed many inconsistencies between web API documentation and their corresponding publicly available specifications. Thus, D2Spec can be used by web API providers to keep documentation and specifications in synchronization.
An IoT Endpoint System-on-Chip for Secure and Energy-Efficient Near-Sensor Analytics
Near-sensor data analytics is a promising direction for IoT endpoints, as it minimizes energy spent on communication and reduces network load - but it also poses security concerns, as valuable data is stored or sent over the network at various stages of the analytics pipeline. Using encryption to protect sensitive data at the boundary of the on-chip analytics engine is a way to address data security issues. To cope with the combined workload of analytics and encryption in a tight power envelope, we propose Fulmine, a System-on-Chip based on a tightly-coupled multi-core cluster augmented with specialized blocks for compute-intensive data processing and encryption functions, supporting software programmability for regular computing tasks. The Fulmine SoC, fabricated in 65nm technology, consumes less than 20mW on average at 0.8V achieving an efficiency of up to 70pJ/B in encryption, 50pJ/px in convolution, or up to 25MIPS/mW in software. As a strong argument for real-life flexible application of our platform, we show experimental results for three secure analytics use cases: secure autonomous aerial surveillance with a state-of-the-art deep CNN consuming 3.16pJ per equivalent RISC op; local CNN-based face detection with secured remote recognition in 5.74pJ/op; and seizure detection with encrypted data collection from EEG within 12.7pJ/op.
Taxonomy Adaptive Cross-Domain Adaptation in Medical Imaging via Optimization Trajectory Distillation
The success of automated medical image analysis depends on large-scale and expert-annotated training sets. Unsupervised domain adaptation (UDA) has been raised as a promising approach to alleviate the burden of labeled data collection. However, they generally operate under the closed-set adaptation setting assuming an identical label set between the source and target domains, which is over-restrictive in clinical practice where new classes commonly exist across datasets due to taxonomic inconsistency. While several methods have been presented to tackle both domain shifts and incoherent label sets, none of them take into account the common characteristics of the two issues and consider the learning dynamics along network training. In this work, we propose optimization trajectory distillation, a unified approach to address the two technical challenges from a new perspective. It exploits the low-rank nature of gradient space and devises a dual-stream distillation algorithm to regularize the learning dynamics of insufficiently annotated domain and classes with the external guidance obtained from reliable sources. Our approach resolves the issue of inadequate navigation along network optimization, which is the major obstacle in the taxonomy adaptive cross-domain adaptation scenario. We evaluate the proposed method extensively on several tasks towards various endpoints with clinical and open-world significance. The results demonstrate its effectiveness and improvements over previous methods.
Sustainable Cloud Services for Verbal Interaction with Embodied Agents
This article presents the design and the implementation of a cloud system for knowledge-based autonomous interaction devised for Social Robots and other conversational agents. The system is particularly convenient for low-cost robots and devices: it can be used as a stand-alone dialogue system or as an integration to provide "background" dialogue capabilities to any preexisting Natural Language Processing ability that the robot may already have as part of its basic skills. By connecting to the cloud, developers are provided with a sustainable solution to manage verbal interaction through a network connection, with about 3,000 topics of conversation ready for "chit-chatting" and a library of pre-cooked plans that only needs to be grounded into the robot's physical capabilities. The system is structured as a set of REST API endpoints so that it can be easily expanded by adding new APIs to improve the capabilities of the clients connected to the cloud. Another key feature of the system is that it has been designed to make the development of its clients straightforward: in this way, multiple robots and devices can be easily endowed with the capability of autonomously interacting with the user, understanding when to perform specific actions, and exploiting all the information provided by cloud services. The article outlines and discusses the results of the experiments performed to assess the system's performance in terms of response time, paving the way for its use both for research and market solutions. Links to repositories with clients for ROS and popular robots such as Pepper and NAO are available on request.
DoraCycle: Domain-Oriented Adaptation of Unified Generative Model in Multimodal Cycles
Adapting generative models to specific domains presents an effective solution for satisfying specialized requirements. However, adapting to some complex domains remains challenging, especially when these domains require substantial paired data to capture the targeted distributions. Since unpaired data from a single modality, such as vision or language, is more readily available, we utilize the bidirectional mappings between vision and language learned by the unified generative model to enable training on unpaired data for domain adaptation. Specifically, we propose DoraCycle, which integrates two multimodal cycles: text-to-image-to-text and image-to-text-to-image. The model is optimized through cross-entropy loss computed at the cycle endpoints, where both endpoints share the same modality. This facilitates self-evolution of the model without reliance on annotated text-image pairs. Experimental results demonstrate that for tasks independent of paired knowledge, such as stylization, DoraCycle can effectively adapt the unified model using only unpaired data. For tasks involving new paired knowledge, such as specific identities, a combination of a small set of paired image-text examples and larger-scale unpaired data is sufficient for effective domain-oriented adaptation. The code will be released at https://github.com/showlab/DoraCycle.
Controllable Diverse Sampling for Diffusion Based Motion Behavior Forecasting
In autonomous driving tasks, trajectory prediction in complex traffic environments requires adherence to real-world context conditions and behavior multimodalities. Existing methods predominantly rely on prior assumptions or generative models trained on curated data to learn road agents' stochastic behavior bounded by scene constraints. However, they often face mode averaging issues due to data imbalance and simplistic priors, and could even suffer from mode collapse due to unstable training and single ground truth supervision. These issues lead the existing methods to a loss of predictive diversity and adherence to the scene constraints. To address these challenges, we introduce a novel trajectory generator named Controllable Diffusion Trajectory (CDT), which integrates map information and social interactions into a Transformer-based conditional denoising diffusion model to guide the prediction of future trajectories. To ensure multimodality, we incorporate behavioral tokens to direct the trajectory's modes, such as going straight, turning right or left. Moreover, we incorporate the predicted endpoints as an alternative behavioral token into the CDT model to facilitate the prediction of accurate trajectories. Extensive experiments on the Argoverse 2 benchmark demonstrate that CDT excels in generating diverse and scene-compliant trajectories in complex urban settings.
Bidirectional Diffusion Bridge Models
Diffusion bridges have shown potential in paired image-to-image (I2I) translation tasks. However, existing methods are limited by their unidirectional nature, requiring separate models for forward and reverse translations. This not only doubles the computational cost but also restricts their practicality. In this work, we introduce the Bidirectional Diffusion Bridge Model (BDBM), a scalable approach that facilitates bidirectional translation between two coupled distributions using a single network. BDBM leverages the Chapman-Kolmogorov Equation for bridges, enabling it to model data distribution shifts across timesteps in both forward and backward directions by exploiting the interchangeability of the initial and target timesteps within this framework. Notably, when the marginal distribution given endpoints is Gaussian, BDBM's transition kernels in both directions possess analytical forms, allowing for efficient learning with a single network. We demonstrate the connection between BDBM and existing bridge methods, such as Doob's h-transform and variational approaches, and highlight its advantages. Extensive experiments on high-resolution I2I translation tasks demonstrate that BDBM not only enables bidirectional translation with minimal additional cost but also outperforms state-of-the-art bridge models. Our source code is available at [https://github.com/kvmduc/BDBM||https://github.com/kvmduc/BDBM].
Packing Input Frame Context in Next-Frame Prediction Models for Video Generation
We present a neural network structure, FramePack, to train next-frame (or next-frame-section) prediction models for video generation. The FramePack compresses input frames to make the transformer context length a fixed number regardless of the video length. As a result, we are able to process a large number of frames using video diffusion with computation bottleneck similar to image diffusion. This also makes the training video batch sizes significantly higher (batch sizes become comparable to image diffusion training). We also propose an anti-drifting sampling method that generates frames in inverted temporal order with early-established endpoints to avoid exposure bias (error accumulation over iterations). Finally, we show that existing video diffusion models can be finetuned with FramePack, and their visual quality may be improved because the next-frame prediction supports more balanced diffusion schedulers with less extreme flow shift timesteps.
API Agents vs. GUI Agents: Divergence and Convergence
Large language models (LLMs) have evolved beyond simple text generation to power software agents that directly translate natural language commands into tangible actions. While API-based LLM agents initially rose to prominence for their robust automation capabilities and seamless integration with programmatic endpoints, recent progress in multimodal LLM research has enabled GUI-based LLM agents that interact with graphical user interfaces in a human-like manner. Although these two paradigms share the goal of enabling LLM-driven task automation, they diverge significantly in architectural complexity, development workflows, and user interaction models. This paper presents the first comprehensive comparative study of API-based and GUI-based LLM agents, systematically analyzing their divergence and potential convergence. We examine key dimensions and highlight scenarios in which hybrid approaches can harness their complementary strengths. By proposing clear decision criteria and illustrating practical use cases, we aim to guide practitioners and researchers in selecting, combining, or transitioning between these paradigms. Ultimately, we indicate that continuing innovations in LLM-based automation are poised to blur the lines between API- and GUI-driven agents, paving the way for more flexible, adaptive solutions in a wide range of real-world applications.
Hallucinating AI Hijacking Attack: Large Language Models and Malicious Code Recommenders
The research builds and evaluates the adversarial potential to introduce copied code or hallucinated AI recommendations for malicious code in popular code repositories. While foundational large language models (LLMs) from OpenAI, Google, and Anthropic guard against both harmful behaviors and toxic strings, previous work on math solutions that embed harmful prompts demonstrate that the guardrails may differ between expert contexts. These loopholes would appear in mixture of expert's models when the context of the question changes and may offer fewer malicious training examples to filter toxic comments or recommended offensive actions. The present work demonstrates that foundational models may refuse to propose destructive actions correctly when prompted overtly but may unfortunately drop their guard when presented with a sudden change of context, like solving a computer programming challenge. We show empirical examples with trojan-hosting repositories like GitHub, NPM, NuGet, and popular content delivery networks (CDN) like jsDelivr which amplify the attack surface. In the LLM's directives to be helpful, example recommendations propose application programming interface (API) endpoints which a determined domain-squatter could acquire and setup attack mobile infrastructure that triggers from the naively copied code. We compare this attack to previous work on context-shifting and contrast the attack surface as a novel version of "living off the land" attacks in the malware literature. In the latter case, foundational language models can hijack otherwise innocent user prompts to recommend actions that violate their owners' safety policies when posed directly without the accompanying coding support request.
Guarded Query Routing for Large Language Models
Query routing, the task to route user queries to different large language model (LLM) endpoints, can be considered as a text classification problem. However, out-of-distribution queries must be handled properly, as those could be about unrelated domains, queries in other languages, or even contain unsafe text. Here, we thus study a guarded query routing problem, for which we first introduce the Guarded Query Routing Benchmark (GQR-Bench, released as Python package gqr), covers three exemplary target domains (law, finance, and healthcare), and seven datasets to test robustness against out-of-distribution queries. We then use GQR-Bench to contrast the effectiveness and efficiency of LLM-based routing mechanisms (GPT-4o-mini, Llama-3.2-3B, and Llama-3.1-8B), standard LLM-based guardrail approaches (LlamaGuard and NVIDIA NeMo Guardrails), continuous bag-of-words classifiers (WideMLP, fastText), and traditional machine learning models (SVM, XGBoost). Our results show that WideMLP, enhanced with out-of-domain detection capabilities, yields the best trade-off between accuracy (88%) and speed (<4ms). The embedding-based fastText excels at speed (<1ms) with acceptable accuracy (80%), whereas LLMs yield the highest accuracy (91%) but are comparatively slow (62ms for local Llama-3.1:8B and 669ms for remote GPT-4o-mini calls). Our findings challenge the automatic reliance on LLMs for (guarded) query routing and provide concrete recommendations for practical applications. Source code is available: https://github.com/williambrach/gqr.
BAMM: Bidirectional Autoregressive Motion Model
Generating human motion from text has been dominated by denoising motion models either through diffusion or generative masking process. However, these models face great limitations in usability by requiring prior knowledge of the motion length. Conversely, autoregressive motion models address this limitation by adaptively predicting motion endpoints, at the cost of degraded generation quality and editing capabilities. To address these challenges, we propose Bidirectional Autoregressive Motion Model (BAMM), a novel text-to-motion generation framework. BAMM consists of two key components: (1) a motion tokenizer that transforms 3D human motion into discrete tokens in latent space, and (2) a masked self-attention transformer that autoregressively predicts randomly masked tokens via a hybrid attention masking strategy. By unifying generative masked modeling and autoregressive modeling, BAMM captures rich and bidirectional dependencies among motion tokens, while learning the probabilistic mapping from textual inputs to motion outputs with dynamically-adjusted motion sequence length. This feature enables BAMM to simultaneously achieving high-quality motion generation with enhanced usability and built-in motion editability. Extensive experiments on HumanML3D and KIT-ML datasets demonstrate that BAMM surpasses current state-of-the-art methods in both qualitative and quantitative measures. Our project page is available at https://exitudio.github.io/BAMM-page
Arrow-Guided VLM: Enhancing Flowchart Understanding via Arrow Direction Encoding
Flowcharts are indispensable tools in software design and business-process analysis, yet current vision-language models (VLMs) frequently misinterpret the directional arrows and graph topology that set these diagrams apart from natural images. We introduce a seven-stage pipeline grouped into three broader processes: (1) arrow-aware detection of nodes and arrow endpoints; (2) optical character recognition (OCR) to extract node text; and (3) construction of a structured prompt that guides the VLMs. Tested on a 90-question benchmark distilled from 30 annotated flowcharts, the method raises overall accuracy from 80 % to 89 % (+9 percentage points) without any task-specific fine-tuning. The gain is most pronounced for next-step queries (25/30 -> 30/30; 100 %, +17 pp); branch-result questions improve more modestly, and before-step questions remain difficult. A parallel evaluation with an LLM-as-a-Judge protocol shows the same trends, reinforcing the advantage of explicit arrow encoding. Limitations include dependence on detector and OCR precision, the small evaluation set, and residual errors at nodes with multiple incoming edges. Future work will enlarge the benchmark with synthetic and handwritten flowcharts and assess the approach on Business Process Model and Notation (BPMN) and Unified Modeling Language (UML).
Visual Re-Ranking with Non-Visual Side Information
The standard approach for visual place recognition is to use global image descriptors to retrieve the most similar database images for a given query image. The results can then be further improved with re-ranking methods that re-order the top scoring images. However, existing methods focus on re-ranking based on the same image descriptors that were used for the initial retrieval, which we argue provides limited additional signal. In this work we propose Generalized Contextual Similarity Aggregation (GCSA), which is a graph neural network-based re-ranking method that, in addition to the visual descriptors, can leverage other types of available side information. This can for example be other sensor data (such as signal strength of nearby WiFi or BlueTooth endpoints) or geometric properties such as camera poses for database images. In many applications this information is already present or can be acquired with low effort. Our architecture leverages the concept of affinity vectors to allow for a shared encoding of the heterogeneous multi-modal input. Two large-scale datasets, covering both outdoor and indoor localization scenarios, are utilized for training and evaluation. In experiments we show significant improvement not only on image retrieval metrics, but also for the downstream visual localization task.
Diffusion Bridge Implicit Models
Denoising diffusion bridge models (DDBMs) are a powerful variant of diffusion models for interpolating between two arbitrary paired distributions given as endpoints. Despite their promising performance in tasks like image translation, DDBMs require a computationally intensive sampling process that involves the simulation of a (stochastic) differential equation through hundreds of network evaluations. In this work, we take the first step in fast sampling of DDBMs without extra training, motivated by the well-established recipes in diffusion models. We generalize DDBMs via a class of non-Markovian diffusion bridges defined on the discretized timesteps concerning sampling, which share the same marginal distributions and training objectives, give rise to generative processes ranging from stochastic to deterministic, and result in diffusion bridge implicit models (DBIMs). DBIMs are not only up to 25times faster than the vanilla sampler of DDBMs but also induce a novel, simple, and insightful form of ordinary differential equation (ODE) which inspires high-order numerical solvers. Moreover, DBIMs maintain the generation diversity in a distinguished way, by using a booting noise in the initial sampling step, which enables faithful encoding, reconstruction, and semantic interpolation in image translation tasks. Code is available at https://github.com/thu-ml/DiffusionBridge.
Deep Geometrized Cartoon Line Inbetweening
We aim to address a significant but understudied problem in the anime industry, namely the inbetweening of cartoon line drawings. Inbetweening involves generating intermediate frames between two black-and-white line drawings and is a time-consuming and expensive process that can benefit from automation. However, existing frame interpolation methods that rely on matching and warping whole raster images are unsuitable for line inbetweening and often produce blurring artifacts that damage the intricate line structures. To preserve the precision and detail of the line drawings, we propose a new approach, AnimeInbet, which geometrizes raster line drawings into graphs of endpoints and reframes the inbetweening task as a graph fusion problem with vertex repositioning. Our method can effectively capture the sparsity and unique structure of line drawings while preserving the details during inbetweening. This is made possible via our novel modules, i.e., vertex geometric embedding, a vertex correspondence Transformer, an effective mechanism for vertex repositioning and a visibility predictor. To train our method, we introduce MixamoLine240, a new dataset of line drawings with ground truth vectorization and matching labels. Our experiments demonstrate that AnimeInbet synthesizes high-quality, clean, and complete intermediate line drawings, outperforming existing methods quantitatively and qualitatively, especially in cases with large motions. Data and code are available at https://github.com/lisiyao21/AnimeInbet.
DiffusionSfM: Predicting Structure and Motion via Ray Origin and Endpoint Diffusion
Current Structure-from-Motion (SfM) methods typically follow a two-stage pipeline, combining learned or geometric pairwise reasoning with a subsequent global optimization step. In contrast, we propose a data-driven multi-view reasoning approach that directly infers 3D scene geometry and camera poses from multi-view images. Our framework, DiffusionSfM, parameterizes scene geometry and cameras as pixel-wise ray origins and endpoints in a global frame and employs a transformer-based denoising diffusion model to predict them from multi-view inputs. To address practical challenges in training diffusion models with missing data and unbounded scene coordinates, we introduce specialized mechanisms that ensure robust learning. We empirically validate DiffusionSfM on both synthetic and real datasets, demonstrating that it outperforms classical and learning-based approaches while naturally modeling uncertainty.
HRET: A Self-Evolving LLM Evaluation Toolkit for Korean
Recent advancements in Korean large language models (LLMs) have spurred numerous benchmarks and evaluation methodologies, yet the lack of a standardized evaluation framework has led to inconsistent results and limited comparability. To address this, we introduce HRET Haerae Evaluation Toolkit, an open-source, self-evolving evaluation framework tailored specifically for Korean LLMs. HRET unifies diverse evaluation methods, including logit-based scoring, exact-match, language-inconsistency penalization, and LLM-as-a-Judge assessments. Its modular, registry-based architecture integrates major benchmarks (HAE-RAE Bench, KMMLU, KUDGE, HRM8K) and multiple inference backends (vLLM, HuggingFace, OpenAI-compatible endpoints). With automated pipelines for continuous evolution, HRET provides a robust foundation for reproducible, fair, and transparent Korean NLP research.
Transformers for molecular property prediction: Domain adaptation efficiently improves performance
Most of the current transformer-based chemical language models are pre-trained on millions to billions of molecules. However, the improvement from such scaling in dataset size is not confidently linked to improved molecular property prediction. The aim of this study is to investigate and overcome some of the limitations of transformer models in predicting molecular properties. Specifically, we examine the impact of pre-training dataset size and diversity on the performance of transformer models and investigate the use of domain adaptation as a technique for improving model performance. First, our findings indicate that increasing pretraining dataset size beyond 400K molecules from the GuacaMol dataset does not result in a significant improvement on four ADME endpoints, namely, solubility, permeability, microsomal stability, and plasma protein binding. Second, our results demonstrate that using domain adaptation by further training the transformer model on a small set of domain-relevant molecules, i.e., a few hundred to a few thousand, using multi-task regression of physicochemical properties was sufficient to significantly improve performance for three out of the four investigated ADME endpoints (P-value < 0.001). Finally, we observe that a model pre-trained on 400K molecules and domain adopted on a few hundred/thousand molecules performs similarly (P-value > 0.05) to more complicated transformer models like MolBERT(pre-trained on 1.3M molecules) and MolFormer (pre-trained on 100M molecules). A comparison to a random forest model trained on basic physicochemical properties showed similar performance to the examined transformer models. We believe that current transformer models can be improved through further systematic analysis of pre-training and downstream data, pre-training objectives, and scaling laws, ultimately leading to better and more helpful models.
Holography of Charged Dilaton Black Holes
We study charged dilaton black branes in AdS_4. Our system involves a dilaton phi coupled to a Maxwell field F_{munu} with dilaton-dependent gauge coupling, {1over g^2} = f^2(phi). First, we find the solutions for extremal and near extremal branes through a combination of analytical and numerical techniques. The near horizon geometries in the simplest cases, where f(phi) = e^{alphaphi}, are Lifshitz-like, with a dynamical exponent z determined by alpha. The black hole thermodynamics varies in an interesting way with alpha, but in all cases the entropy is vanishing and the specific heat is positive for the near extremal solutions. We then compute conductivity in these backgrounds. We find that somewhat surprisingly, the AC conductivity vanishes like omega^2 at T=0 independent of alpha. We also explore the charged black brane physics of several other classes of gauge-coupling functions f(phi). In addition to possible applications in AdS/CMT, the extremal black branes are of interest from the point of view of the attractor mechanism. The near horizon geometries for these branes are universal, independent of the asymptotic values of the moduli, and describe generic classes of endpoints for attractor flows which are different from AdS_2times R^2.
Denoising Diffusion Bridge Models
Diffusion models are powerful generative models that map noise to data using stochastic processes. However, for many applications such as image editing, the model input comes from a distribution that is not random noise. As such, diffusion models must rely on cumbersome methods like guidance or projected sampling to incorporate this information in the generative process. In our work, we propose Denoising Diffusion Bridge Models (DDBMs), a natural alternative to this paradigm based on diffusion bridges, a family of processes that interpolate between two paired distributions given as endpoints. Our method learns the score of the diffusion bridge from data and maps from one endpoint distribution to the other by solving a (stochastic) differential equation based on the learned score. Our method naturally unifies several classes of generative models, such as score-based diffusion models and OT-Flow-Matching, allowing us to adapt existing design and architectural choices to our more general problem. Empirically, we apply DDBMs to challenging image datasets in both pixel and latent space. On standard image translation problems, DDBMs achieve significant improvement over baseline methods, and, when we reduce the problem to image generation by setting the source distribution to random noise, DDBMs achieve comparable FID scores to state-of-the-art methods despite being built for a more general task.
RankVicuna: Zero-Shot Listwise Document Reranking with Open-Source Large Language Models
Researchers have successfully applied large language models (LLMs) such as ChatGPT to reranking in an information retrieval context, but to date, such work has mostly been built on proprietary models hidden behind opaque API endpoints. This approach yields experimental results that are not reproducible and non-deterministic, threatening the veracity of outcomes that build on such shaky foundations. To address this significant shortcoming, we present RankVicuna, the first fully open-source LLM capable of performing high-quality listwise reranking in a zero-shot setting. Experimental results on the TREC 2019 and 2020 Deep Learning Tracks show that we can achieve effectiveness comparable to zero-shot reranking with GPT-3.5 with a much smaller 7B parameter model, although our effectiveness remains slightly behind reranking with GPT-4. We hope our work provides the foundation for future research on reranking with modern LLMs. All the code necessary to reproduce our results is available at https://github.com/castorini/rank_llm.
RetroBridge: Modeling Retrosynthesis with Markov Bridges
Retrosynthesis planning is a fundamental challenge in chemistry which aims at designing reaction pathways from commercially available starting materials to a target molecule. Each step in multi-step retrosynthesis planning requires accurate prediction of possible precursor molecules given the target molecule and confidence estimates to guide heuristic search algorithms. We model single-step retrosynthesis planning as a distribution learning problem in a discrete state space. First, we introduce the Markov Bridge Model, a generative framework aimed to approximate the dependency between two intractable discrete distributions accessible via a finite sample of coupled data points. Our framework is based on the concept of a Markov bridge, a Markov process pinned at its endpoints. Unlike diffusion-based methods, our Markov Bridge Model does not need a tractable noise distribution as a sampling proxy and directly operates on the input product molecules as samples from the intractable prior distribution. We then address the retrosynthesis planning problem with our novel framework and introduce RetroBridge, a template-free retrosynthesis modeling approach that achieves state-of-the-art results on standard evaluation benchmarks.
Analyzing Learned Molecular Representations for Property Prediction
Advancements in neural machinery have led to a wide range of algorithmic solutions for molecular property prediction. Two classes of models in particular have yielded promising results: neural networks applied to computed molecular fingerprints or expert-crafted descriptors, and graph convolutional neural networks that construct a learned molecular representation by operating on the graph structure of the molecule. However, recent literature has yet to clearly determine which of these two methods is superior when generalizing to new chemical space. Furthermore, prior research has rarely examined these new models in industry research settings in comparison to existing employed models. In this paper, we benchmark models extensively on 19 public and 16 proprietary industrial datasets spanning a wide variety of chemical endpoints. In addition, we introduce a graph convolutional model that consistently matches or outperforms models using fixed molecular descriptors as well as previous graph neural architectures on both public and proprietary datasets. Our empirical findings indicate that while approaches based on these representations have yet to reach the level of experimental reproducibility, our proposed model nevertheless offers significant improvements over models currently used in industrial workflows.
