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Multi-scale Iterative Refinement towards Robust and Versatile Molecular Docking

Molecular docking is a key computational tool utilized to predict the binding conformations of small molecules to protein targets, which is fundamental in the design of novel drugs. Despite recent advancements in geometric deep learning-based approaches leading to improvements in blind docking efficiency, these methods have encountered notable challenges, such as limited generalization performance on unseen proteins, the inability to concurrently address the settings of blind docking and site-specific docking, and the frequent occurrence of physical implausibilities such as inter-molecular steric clash. In this study, we introduce DeltaDock, a robust and versatile framework designed for efficient molecular docking to overcome these challenges. DeltaDock operates in a two-step process: rapid initial complex structures sampling followed by multi-scale iterative refinement of the initial structures. In the initial stage, to sample accurate structures with high efficiency, we develop a ligand-dependent binding site prediction model founded on large protein models and graph neural networks. This model is then paired with GPU-accelerated sampling algorithms. The sampled structures are updated using a multi-scale iterative refinement module that captures both protein-ligand atom-atom interactions and residue-atom interactions in the following stage. Distinct from previous geometric deep learning methods that are conditioned on the blind docking setting, DeltaDock demonstrates superior performance in both blind docking and site-specific docking settings. Comprehensive experimental results reveal that DeltaDock consistently surpasses baseline methods in terms of docking accuracy. Furthermore, it displays remarkable generalization capabilities and proficiency for predicting physically valid structures, thereby attesting to its robustness and reliability in various scenarios.

FastEdit: Fast Text-Guided Single-Image Editing via Semantic-Aware Diffusion Fine-Tuning

Conventional Text-guided single-image editing approaches require a two-step process, including fine-tuning the target text embedding for over 1K iterations and the generative model for another 1.5K iterations. Although it ensures that the resulting image closely aligns with both the input image and the target text, this process often requires 7 minutes per image, posing a challenge for practical application due to its time-intensive nature. To address this bottleneck, we introduce FastEdit, a fast text-guided single-image editing method with semantic-aware diffusion fine-tuning, dramatically accelerating the editing process to only 17 seconds. FastEdit streamlines the generative model's fine-tuning phase, reducing it from 1.5K to a mere 50 iterations. For diffusion fine-tuning, we adopt certain time step values based on the semantic discrepancy between the input image and target text. Furthermore, FastEdit circumvents the initial fine-tuning step by utilizing an image-to-image model that conditions on the feature space, rather than the text embedding space. It can effectively align the target text prompt and input image within the same feature space and save substantial processing time. Additionally, we apply the parameter-efficient fine-tuning technique LoRA to U-net. With LoRA, FastEdit minimizes the model's trainable parameters to only 0.37\% of the original size. At the same time, we can achieve comparable editing outcomes with significantly reduced computational overhead. We conduct extensive experiments to validate the editing performance of our approach and show promising editing capabilities, including content addition, style transfer, background replacement, and posture manipulation, etc.

Bit Cipher -- A Simple yet Powerful Word Representation System that Integrates Efficiently with Language Models

While Large Language Models (LLMs) become ever more dominant, classic pre-trained word embeddings sustain their relevance through computational efficiency and nuanced linguistic interpretation. Drawing from recent studies demonstrating that the convergence of GloVe and word2vec optimizations all tend towards log-co-occurrence matrix variants, we construct a novel word representation system called Bit-cipher that eliminates the need of backpropagation while leveraging contextual information and hyper-efficient dimensionality reduction techniques based on unigram frequency, providing strong interpretability, alongside efficiency. We use the bit-cipher algorithm to train word vectors via a two-step process that critically relies on a hyperparameter -- bits -- that controls the vector dimension. While the first step trains the bit-cipher, the second utilizes it under two different aggregation modes -- summation or concatenation -- to produce contextually rich representations from word co-occurrences. We extend our investigation into bit-cipher's efficacy, performing probing experiments on part-of-speech (POS) tagging and named entity recognition (NER) to assess its competitiveness with classic embeddings like word2vec and GloVe. Additionally, we explore its applicability in LM training and fine-tuning. By replacing embedding layers with cipher embeddings, our experiments illustrate the notable efficiency of cipher in accelerating the training process and attaining better optima compared to conventional training paradigms. Experiments on the integration of bit-cipher embedding layers with Roberta, T5, and OPT, prior to or as a substitute for fine-tuning, showcase a promising enhancement to transfer learning, allowing rapid model convergence while preserving competitive performance.

DocCGen: Document-based Controlled Code Generation

Recent developments show that Large Language Models (LLMs) produce state-of-the-art performance on natural language (NL) to code generation for resource-rich general-purpose languages like C++, Java, and Python. However, their practical usage for structured domain-specific languages (DSLs) such as YAML, JSON is limited due to domain-specific schema, grammar, and customizations generally unseen by LLMs during pre-training. Efforts have been made to mitigate this challenge via in-context learning through relevant examples or by fine-tuning. However, it suffers from problems, such as limited DSL samples and prompt sensitivity but enterprises maintain good documentation of the DSLs. Therefore, we propose DocCGen, a framework that can leverage such rich knowledge by breaking the NL-to-Code generation task for structured code languages into a two-step process. First, it detects the correct libraries using the library documentation that best matches the NL query. Then, it utilizes schema rules extracted from the documentation of these libraries to constrain the decoding. We evaluate our framework for two complex structured languages, Ansible YAML and Bash command, consisting of two settings: Out-of-domain (OOD) and In-domain (ID). Our extensive experiments show that DocCGen consistently improves different-sized language models across all six evaluation metrics, reducing syntactic and semantic errors in structured code. We plan to open-source the datasets and code to motivate research in constrained code generation.

Evidence to Generate (E2G): A Single-agent Two-step Prompting for Context Grounded and Retrieval Augmented Reasoning

While chain-of-thought (CoT) prompting has revolutionized how LLMs perform reasoning tasks, its current methods and variations (e.g, Self-consistency, ReACT, Reflexion, Tree-of-Thoughts (ToT), Cumulative Reasoning (CR)) suffer from limitations like slowness, limited context grounding, hallucination and inconsistent outputs. To overcome these challenges, we introduce Evidence to Generate (E2G), a novel single-agent, two-step prompting framework. Instead of unverified reasoning claims, this innovative approach leverages the power of "evidence for decision making" by first focusing exclusively on the thought sequences (the series of intermediate steps) explicitly mentioned in the context which then serve as extracted evidence, guiding the LLM's output generation process with greater precision and efficiency. This simple yet powerful approach unlocks the true potential of chain-of-thought like prompting, paving the way for faster, more reliable, and more contextually aware reasoning in LLMs. \tool achieves remarkable results robustly across a wide range of knowledge-intensive reasoning and generation tasks, surpassing baseline approaches with state-of-the-art LLMs. For example, (i) on LogiQA benchmark using GPT-4 as backbone model, \tool achieves a new state-of-the Accuracy of 53.8% exceeding CoT by 18%, ToT by 11%, CR by 9% (ii) a variant of E2G with PaLM2 outperforms the variable-shot performance of Gemini Ultra by 0.9 F1 points, reaching an F1 score of 83.3 on a subset of DROP.

Towards Automatic Boundary Detection for Human-AI Collaborative Hybrid Essay in Education

The recent large language models (LLMs), e.g., ChatGPT, have been able to generate human-like and fluent responses when provided with specific instructions. While admitting the convenience brought by technological advancement, educators also have concerns that students might leverage LLMs to complete their writing assignments and pass them off as their original work. Although many AI content detection studies have been conducted as a result of such concerns, most of these prior studies modeled AI content detection as a classification problem, assuming that a text is either entirely human-written or entirely AI-generated. In this study, we investigated AI content detection in a rarely explored yet realistic setting where the text to be detected is collaboratively written by human and generative LLMs (i.e., hybrid text). We first formalized the detection task as identifying the transition points between human-written content and AI-generated content from a given hybrid text (boundary detection). Then we proposed a two-step approach where we (1) separated AI-generated content from human-written content during the encoder training process; and (2) calculated the distances between every two adjacent prototypes and assumed that the boundaries exist between the two adjacent prototypes that have the furthest distance from each other. Through extensive experiments, we observed the following main findings: (1) the proposed approach consistently outperformed the baseline methods across different experiment settings; (2) the encoder training process can significantly boost the performance of the proposed approach; (3) when detecting boundaries for single-boundary hybrid essays, the proposed approach could be enhanced by adopting a relatively large prototype size, leading to a 22% improvement in the In-Domain evaluation and an 18% improvement in the Out-of-Domain evaluation.

MagicClay: Sculpting Meshes With Generative Neural Fields

The recent developments in neural fields have brought phenomenal capabilities to the field of shape generation, but they lack crucial properties, such as incremental control - a fundamental requirement for artistic work. Triangular meshes, on the other hand, are the representation of choice for most geometry related tasks, offering efficiency and intuitive control, but do not lend themselves to neural optimization. To support downstream tasks, previous art typically proposes a two-step approach, where first a shape is generated using neural fields, and then a mesh is extracted for further processing. Instead, in this paper we introduce a hybrid approach that maintains both a mesh and a Signed Distance Field (SDF) representations consistently. Using this representation, we introduce MagicClay - an artist friendly tool for sculpting regions of a mesh according to textual prompts while keeping other regions untouched. Our framework carefully and efficiently balances consistency between the representations and regularizations in every step of the shape optimization; Relying on the mesh representation, we show how to render the SDF at higher resolutions and faster. In addition, we employ recent work in differentiable mesh reconstruction to adaptively allocate triangles in the mesh where required, as indicated by the SDF. Using an implemented prototype, we demonstrate superior generated geometry compared to the state-of-the-art, and novel consistent control, allowing sequential prompt-based edits to the same mesh for the first time.

Dynamic Prompt Learning via Policy Gradient for Semi-structured Mathematical Reasoning

Mathematical reasoning, a core ability of human intelligence, presents unique challenges for machines in abstract thinking and logical reasoning. Recent large pre-trained language models such as GPT-3 have achieved remarkable progress on mathematical reasoning tasks written in text form, such as math word problems (MWP). However, it is unknown if the models can handle more complex problems that involve math reasoning over heterogeneous information, such as tabular data. To fill the gap, we present Tabular Math Word Problems (TabMWP), a new dataset containing 38,431 open-domain grade-level problems that require mathematical reasoning on both textual and tabular data. Each question in TabMWP is aligned with a tabular context, which is presented as an image, semi-structured text, and a structured table. There are two types of questions: free-text and multi-choice, and each problem is annotated with gold solutions to reveal the multi-step reasoning process. We evaluate different pre-trained models on TabMWP, including the GPT-3 model in a few-shot setting. As earlier studies suggest, since few-shot GPT-3 relies on the selection of in-context examples, its performance is unstable and can degrade to near chance. The unstable issue is more severe when handling complex problems like TabMWP. To mitigate this, we further propose a novel approach, PromptPG, which utilizes policy gradient to learn to select in-context examples from a small amount of training data and then constructs the corresponding prompt for the test example. Experimental results show that our method outperforms the best baseline by 5.31% on the accuracy metric and reduces the prediction variance significantly compared to random selection, which verifies its effectiveness in selecting in-context examples.

Invertible Diffusion Models for Compressed Sensing

While deep neural networks (NN) significantly advance image compressed sensing (CS) by improving reconstruction quality, the necessity of training current CS NNs from scratch constrains their effectiveness and hampers rapid deployment. Although recent methods utilize pre-trained diffusion models for image reconstruction, they struggle with slow inference and restricted adaptability to CS. To tackle these challenges, this paper proposes Invertible Diffusion Models (IDM), a novel efficient, end-to-end diffusion-based CS method. IDM repurposes a large-scale diffusion sampling process as a reconstruction model, and fine-tunes it end-to-end to recover original images directly from CS measurements, moving beyond the traditional paradigm of one-step noise estimation learning. To enable such memory-intensive end-to-end fine-tuning, we propose a novel two-level invertible design to transform both (1) multi-step sampling process and (2) noise estimation U-Net in each step into invertible networks. As a result, most intermediate features are cleared during training to reduce up to 93.8% GPU memory. In addition, we develop a set of lightweight modules to inject measurements into noise estimator to further facilitate reconstruction. Experiments demonstrate that IDM outperforms existing state-of-the-art CS networks by up to 2.64dB in PSNR. Compared to the recent diffusion-based approach DDNM, our IDM achieves up to 10.09dB PSNR gain and 14.54 times faster inference. Code is available at https://github.com/Guaishou74851/IDM.

ProcessBench: Identifying Process Errors in Mathematical Reasoning

As language models regularly make mistakes when solving math problems, automated identification of errors in the reasoning process becomes increasingly significant for their scalable oversight. In this paper, we introduce ProcessBench for measuring the ability to identify erroneous steps in mathematical reasoning. It consists of 3,400 test cases, primarily focused on competition- and Olympiad-level math problems. Each test case contains a step-by-step solution with error location annotated by human experts. Models are required to identify the earliest step that contains an error, or conclude that all steps are correct. We conduct extensive evaluation on ProcessBench, involving two types of models: process reward models (PRMs) and critic models, where for the latter we prompt general language models to critique each solution step by step. We draw two main observations: (1) Existing PRMs typically fail to generalize to more challenging math problems beyond GSM8K and MATH. They underperform both critic models (i.e., prompted general language models) and our own trained PRM that is straightforwardly fine-tuned on the PRM800K dataset. (2) The best open-source model, QwQ-32B-Preview, has demonstrated the critique capability competitive with the proprietary model GPT-4o, despite that it still lags behind the reasoning-specialized o1-mini. We hope ProcessBench can foster future research in reasoning process assessment, paving the way toward scalable oversight of language models.

Self-Taught Agentic Long Context Understanding

Answering complex, long-context questions remains a major challenge for large language models (LLMs) as it requires effective question clarifications and context retrieval. We propose Agentic Long-Context Understanding (AgenticLU), a framework designed to enhance an LLM's understanding of such queries by integrating targeted self-clarification with contextual grounding within an agentic workflow. At the core of AgenticLU is Chain-of-Clarifications (CoC), where models refine their understanding through self-generated clarification questions and corresponding contextual groundings. By scaling inference as a tree search where each node represents a CoC step, we achieve 97.8% answer recall on NarrativeQA with a search depth of up to three and a branching factor of eight. To amortize the high cost of this search process to training, we leverage the preference pairs for each step obtained by the CoC workflow and perform two-stage model finetuning: (1) supervised finetuning to learn effective decomposition strategies, and (2) direct preference optimization to enhance reasoning quality. This enables AgenticLU models to generate clarifications and retrieve relevant context effectively and efficiently in a single inference pass. Extensive experiments across seven long-context tasks demonstrate that AgenticLU significantly outperforms state-of-the-art prompting methods and specialized long-context LLMs, achieving robust multi-hop reasoning while sustaining consistent performance as context length grows.

rStar-Math: Small LLMs Can Master Math Reasoning with Self-Evolved Deep Thinking

We present rStar-Math to demonstrate that small language models (SLMs) can rival or even surpass the math reasoning capability of OpenAI o1, without distillation from superior models. rStar-Math achieves this by exercising "deep thinking" through Monte Carlo Tree Search (MCTS), where a math policy SLM performs test-time search guided by an SLM-based process reward model. rStar-Math introduces three innovations to tackle the challenges in training the two SLMs: (1) a novel code-augmented CoT data sythesis method, which performs extensive MCTS rollouts to generate step-by-step verified reasoning trajectories used to train the policy SLM; (2) a novel process reward model training method that avoids na\"ive step-level score annotation, yielding a more effective process preference model (PPM); (3) a self-evolution recipe in which the policy SLM and PPM are built from scratch and iteratively evolved to improve reasoning capabilities. Through 4 rounds of self-evolution with millions of synthesized solutions for 747k math problems, rStar-Math boosts SLMs' math reasoning to state-of-the-art levels. On the MATH benchmark, it improves Qwen2.5-Math-7B from 58.8% to 90.0% and Phi3-mini-3.8B from 41.4% to 86.4%, surpassing o1-preview by +4.5% and +0.9%. On the USA Math Olympiad (AIME), rStar-Math solves an average of 53.3% (8/15) of problems, ranking among the top 20% the brightest high school math students. Code and data will be available at https://github.com/microsoft/rStar.

ENAT: Rethinking Spatial-temporal Interactions in Token-based Image Synthesis

Recently, token-based generation have demonstrated their effectiveness in image synthesis. As a representative example, non-autoregressive Transformers (NATs) can generate decent-quality images in a few steps. NATs perform generation in a progressive manner, where the latent tokens of a resulting image are incrementally revealed. At each step, the unrevealed image regions are padded with mask tokens and inferred by NAT. In this paper, we delve into the mechanisms behind the effectiveness of NATs and uncover two important patterns that naturally emerge from NATs: Spatially (within a step), although mask and visible tokens are processed uniformly by NATs, the interactions between them are highly asymmetric. In specific, mask tokens mainly gather information for decoding, while visible tokens tend to primarily provide information, and their deep representations can be built only upon themselves. Temporally (across steps), the interactions between adjacent generation steps mostly concentrate on updating the representations of a few critical tokens, while the computation for the majority of tokens is generally repetitive. Driven by these findings, we propose EfficientNAT (ENAT), a NAT model that explicitly encourages these critical interactions inherent in NATs. At the spatial level, we disentangle the computations of visible and mask tokens by encoding visible tokens independently, while decoding mask tokens conditioned on the fully encoded visible tokens. At the temporal level, we prioritize the computation of the critical tokens at each step, while maximally reusing previously computed token representations to supplement necessary information. ENAT improves the performance of NATs notably with significantly reduced computational cost. Experiments on ImageNet-256, ImageNet-512 and MS-COCO validate the effectiveness of ENAT. Code is available at https://github.com/LeapLabTHU/ENAT.

Concurrent Adversarial Learning for Large-Batch Training

Large-batch training has become a commonly used technique when training neural networks with a large number of GPU/TPU processors. As batch size increases, stochastic optimizers tend to converge to sharp local minima, leading to degraded test performance. Current methods usually use extensive data augmentation to increase the batch size, but we found the performance gain with data augmentation decreases as batch size increases, and data augmentation will become insufficient after certain point. In this paper, we propose to use adversarial learning to increase the batch size in large-batch training. Despite being a natural choice for smoothing the decision surface and biasing towards a flat region, adversarial learning has not been successfully applied in large-batch training since it requires at least two sequential gradient computations at each step, which will at least double the running time compared with vanilla training even with a large number of processors. To overcome this issue, we propose a novel Concurrent Adversarial Learning (ConAdv) method that decouple the sequential gradient computations in adversarial learning by utilizing staled parameters. Experimental results demonstrate that ConAdv can successfully increase the batch size on ResNet-50 training on ImageNet while maintaining high accuracy. In particular, we show ConAdv along can achieve 75.3\% top-1 accuracy on ImageNet ResNet-50 training with 96K batch size, and the accuracy can be further improved to 76.2\% when combining ConAdv with data augmentation. This is the first work successfully scales ResNet-50 training batch size to 96K.

AutoDiffusion: Training-Free Optimization of Time Steps and Architectures for Automated Diffusion Model Acceleration

Diffusion models are emerging expressive generative models, in which a large number of time steps (inference steps) are required for a single image generation. To accelerate such tedious process, reducing steps uniformly is considered as an undisputed principle of diffusion models. We consider that such a uniform assumption is not the optimal solution in practice; i.e., we can find different optimal time steps for different models. Therefore, we propose to search the optimal time steps sequence and compressed model architecture in a unified framework to achieve effective image generation for diffusion models without any further training. Specifically, we first design a unified search space that consists of all possible time steps and various architectures. Then, a two stage evolutionary algorithm is introduced to find the optimal solution in the designed search space. To further accelerate the search process, we employ FID score between generated and real samples to estimate the performance of the sampled examples. As a result, the proposed method is (i).training-free, obtaining the optimal time steps and model architecture without any training process; (ii). orthogonal to most advanced diffusion samplers and can be integrated to gain better sample quality. (iii). generalized, where the searched time steps and architectures can be directly applied on different diffusion models with the same guidance scale. Experimental results show that our method achieves excellent performance by using only a few time steps, e.g. 17.86 FID score on ImageNet 64 times 64 with only four steps, compared to 138.66 with DDIM. The code is available at https://github.com/lilijiangg/AutoDiffusion.

An Experience Report on Machine Learning Reproducibility: Guidance for Practitioners and TensorFlow Model Garden Contributors

Machine learning techniques are becoming a fundamental tool for scientific and engineering progress. These techniques are applied in contexts as diverse as astronomy and spam filtering. However, correctly applying these techniques requires careful engineering. Much attention has been paid to the technical potential; relatively little attention has been paid to the software engineering process required to bring research-based machine learning techniques into practical utility. Technology companies have supported the engineering community through machine learning frameworks such as TensorFLow and PyTorch, but the details of how to engineer complex machine learning models in these frameworks have remained hidden. To promote best practices within the engineering community, academic institutions and Google have partnered to launch a Special Interest Group on Machine Learning Models (SIGMODELS) whose goal is to develop exemplary implementations of prominent machine learning models in community locations such as the TensorFlow Model Garden (TFMG). The purpose of this report is to define a process for reproducing a state-of-the-art machine learning model at a level of quality suitable for inclusion in the TFMG. We define the engineering process and elaborate on each step, from paper analysis to model release. We report on our experiences implementing the YOLO model family with a team of 26 student researchers, share the tools we developed, and describe the lessons we learned along the way.

Opus: A Large Work Model for Complex Workflow Generation

This paper introduces Opus, a novel framework for generating and optimizing Workflows tailored to complex Business Process Outsourcing (BPO) use cases, focusing on cost reduction and quality enhancement while adhering to established industry processes and operational constraints. Our approach generates executable Workflows from Intention, defined as the alignment of Client Input, Client Output, and Process Context. These Workflows are represented as Directed Acyclic Graphs (DAGs), with nodes as Tasks consisting of sequences of executable Instructions, including tools and human expert reviews. We adopt a two-phase methodology: Workflow Generation and Workflow Optimization. In the Generation phase, Workflows are generated using a Large Work Model (LWM) informed by a Work Knowledge Graph (WKG) that encodes domain-specific procedural and operational knowledge. In the Optimization phase, Workflows are transformed into Workflow Graphs (WFGs), where optimal Workflows are determined through path optimization. Our experiments demonstrate that state-of-the-art Large Language Models (LLMs) face challenges in reliably retrieving detailed process data as well as generating industry-compliant workflows. The key contributions of this paper include: - The integration of a Work Knowledge Graph (WKG) into a Large Work Model (LWM), enabling the generation of context-aware, semantically aligned, structured and auditable Workflows. - A two-phase approach that combines Workflow Generation from Intention with graph-based Workflow Optimization. - Opus Alpha 1 Large and Opus Alpha 1 Small, models that outperform state-of-the-art LLMs by 38\% and 29\% respectively in Workflow Generation for a Medical Coding use case.

Alleviating Exposure Bias in Diffusion Models through Sampling with Shifted Time Steps

Diffusion Probabilistic Models (DPM) have shown remarkable efficacy in the synthesis of high-quality images. However, their inference process characteristically requires numerous, potentially hundreds, of iterative steps, which could exaggerate the problem of exposure bias due to the training and inference discrepancy. Previous work has attempted to mitigate this issue by perturbing inputs during training, which consequently mandates the retraining of the DPM. In this work, we conduct a systematic study of exposure bias in DPM and, intriguingly, we find that the exposure bias could be alleviated with a novel sampling method that we propose, without retraining the model. We empirically and theoretically show that, during inference, for each backward time step t and corresponding state x_t, there might exist another time step t_s which exhibits superior coupling with x_t. Based on this finding, we introduce a sampling method named Time-Shift Sampler. Our framework can be seamlessly integrated to existing sampling algorithms, such as DDPM, DDIM and other high-order solvers, inducing merely minimal additional computations. Experimental results show our method brings significant and consistent improvements in FID scores on different datasets and sampling methods. For example, integrating Time-Shift Sampler to F-PNDM yields a FID=3.88, achieving 44.49\% improvements as compared to F-PNDM, on CIFAR-10 with 10 sampling steps, which is more performant than the vanilla DDIM with 100 sampling steps. Our code is available at https://github.com/Mingxiao-Li/TS-DPM.