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Dec 11

Paper2Code: Automating Code Generation from Scientific Papers in Machine Learning

Despite the rapid growth of machine learning research, corresponding code implementations are often unavailable, making it slow and labor-intensive for researchers to reproduce results and build upon prior work. In the meantime, recent Large Language Models (LLMs) excel at understanding scientific documents and generating high-quality code. Inspired by this, we introduce PaperCoder, a multi-agent LLM framework that transforms machine learning papers into functional code repositories. PaperCoder operates in three stages: planning, where it constructs a high-level roadmap, designs the system architecture with diagrams, identifies file dependencies, and generates configuration files; analysis, which focuses on interpreting implementation-specific details; and generation, where modular, dependency-aware code is produced. Moreover, each phase is instantiated through a set of specialized agents designed to collaborate effectively across the pipeline. We then evaluate PaperCoder on generating code implementations from machine learning papers based on both model-based and human evaluations, specifically from the original paper authors, with author-released repositories as ground truth if available. Our results demonstrate the effectiveness of PaperCoder in creating high-quality, faithful implementations. Furthermore, it consistently shows strengths in the recently released PaperBench benchmark, surpassing strong baselines by substantial margins.

  • 4 authors
·
Apr 23 6

AceCoder: Utilizing Existing Code to Enhance Code Generation

Large Language Models (LLMs) have shown great success in code generation. LLMs take as the input a prompt and output the code. A key question is how to make prompts (i.e., Prompting Techniques). Existing prompting techniques are designed for natural language generation and have low accuracy in code generation. In this paper, we propose a new prompting technique named AceCoder. Our motivation is that code generation meets two unique challenges (i.e., requirement understanding and code implementation). AceCoder contains two novel mechanisms (i.e., guided code generation and example retrieval) to solve these challenges. (1) Guided code generation asks LLMs first to analyze requirements and output an intermediate preliminary (e.g., test cases). The preliminary is used to clarify requirements and tell LLMs "what to write". (2) Example retrieval selects similar programs as examples in prompts, which provide lots of relevant content (e.g., algorithms, APIs) and teach LLMs "how to write". We apply AceCoder to three LLMs (e.g., Codex) and evaluate it on three public benchmarks using the Pass@k. Results show that AceCoder can significantly improve the performance of LLMs on code generation. (1) In terms of Pass@1, AceCoder outperforms the state-of-the-art baseline by up to 56.4% in MBPP, 70.7% in MBJP, and 88.4% in MBJSP. (2) AceCoder is effective in LLMs with different sizes (i.e., 6B to 13B) and different languages (i.e., Python, Java, and JavaScript). (3) Human evaluation shows human developers prefer programs from AceCoder.

  • 5 authors
·
Mar 30, 2023

TENET: Leveraging Tests Beyond Validation for Code Generation

Test-Driven Development (TDD) is a widely adopted software engineering practice that requires developers to create and execute tests alongside code implementation, ensuring that software behavior is continuously validated and refined. In the era of vibe coding, where developers increasingly delegate code writing to large language models (LLMs) by specifying high-level intentions, TDD becomes even more crucial, as test cases serve as executable specifications that explicitly define and verify intended functionality beyond what natural-language descriptions and code context can convey. While vibe coding under TDD is promising, there are three main challenges: (1) selecting a small yet effective test suite to improve the generation accuracy and control the execution workload, (2) retrieving context such as relevant code effectively, and (3) systematically using test feedback for effective code refinement. To address these challenges, we introduce TENET, an LLM agent for generating functions in complex real-world repositories under the TDD setting. TENET features three components: (1) a novel test harness mechanism that selects a concise test suite to maximize diversity of target usage scenarios; (2) a tailored agent toolset that performs efficient retrieval of relevant code with interactive debugging; and (3) a reflection-based refinement workflow that iteratively analyzes failures, replenishes context, and applies code refinement. TENET achieves 69.08% and 81.77% Pass@1 on RepoCod and RepoEval benchmarks, outperforming the best agentic baselines by 9.49 and 2.17 percentage points, respectively. In addition, this is the first study of test-driven code generation with repository-level context, examining how different aspects of test suites affect the performance of LLM agents under the TDD setting.

Spec2RTL-Agent: Automated Hardware Code Generation from Complex Specifications Using LLM Agent Systems

Despite recent progress in generating hardware RTL code with LLMs, existing solutions still suffer from a substantial gap between practical application scenarios and the requirements of real-world RTL code development. Prior approaches either focus on overly simplified hardware descriptions or depend on extensive human guidance to process complex specifications, limiting their scalability and automation potential. In this paper, we address this gap by proposing an LLM agent system, termed Spec2RTL-Agent, designed to directly process complex specification documentation and generate corresponding RTL code implementations, advancing LLM-based RTL code generation toward more realistic application settings. To achieve this goal, Spec2RTL-Agent introduces a novel multi-agent collaboration framework that integrates three key enablers: (1) a reasoning and understanding module that translates specifications into structured, step-by-step implementation plans; (2) a progressive coding and prompt optimization module that iteratively refines the code across multiple representations to enhance correctness and synthesisability for RTL conversion; and (3) an adaptive reflection module that identifies and traces the source of errors during generation, ensuring a more robust code generation flow. Instead of directly generating RTL from natural language, our system strategically generates synthesizable C++ code, which is then optimized for HLS. This agent-driven refinement ensures greater correctness and compatibility compared to naive direct RTL generation approaches. We evaluate Spec2RTL-Agent on three specification documents, showing it generates accurate RTL code with up to 75% fewer human interventions than existing methods. This highlights its role as the first fully automated multi-agent system for RTL generation from unstructured specs, reducing reliance on human effort in hardware design.

  • 6 authors
·
Jun 16 2

Swin-X2S: Reconstructing 3D Shape from 2D Biplanar X-ray with Swin Transformers

The conversion from 2D X-ray to 3D shape holds significant potential for improving diagnostic efficiency and safety. However, existing reconstruction methods often rely on hand-crafted features, manual intervention, and prior knowledge, resulting in unstable shape errors and additional processing costs. In this paper, we introduce Swin-X2S, an end-to-end deep learning method for directly reconstructing 3D segmentation and labeling from 2D biplanar orthogonal X-ray images. Swin-X2S employs an encoder-decoder architecture: the encoder leverages 2D Swin Transformer for X-ray information extraction, while the decoder employs 3D convolution with cross-attention to integrate structural features from orthogonal views. A dimension-expanding module is introduced to bridge the encoder and decoder, ensuring a smooth conversion from 2D pixels to 3D voxels. We evaluate proposed method through extensive qualitative and quantitative experiments across nine publicly available datasets covering four anatomies (femur, hip, spine, and rib), with a total of 54 categories. Significant improvements over previous methods have been observed not only in the segmentation and labeling metrics but also in the clinically relevant parameters that are of primary concern in practical applications, which demonstrates the promise of Swin-X2S to provide an effective option for anatomical shape reconstruction in clinical scenarios. Code implementation is available at: https://github.com/liukuan5625/Swin-X2S.

  • 11 authors
·
Jan 10

On-device Sora: Enabling Diffusion-Based Text-to-Video Generation for Mobile Devices

We present On-device Sora, a first pioneering solution for diffusion-based on-device text-to-video generation that operates efficiently on smartphone-grade devices. Building on Open-Sora, On-device Sora applies three novel techniques to address the challenges of diffusion-based text-to-video generation on computation- and memory-limited mobile devices. First, Linear Proportional Leap (LPL) reduces the excessive denoising steps required in video diffusion through an efficient leap-based approach. Second, Temporal Dimension Token Merging (TDTM) minimizes intensive token-processing computation in attention layers by merging consecutive tokens along the temporal dimension. Third, Concurrent Inference with Dynamic Loading (CI-DL) dynamically partitions large models into smaller blocks and loads them into memory for concurrent model inference, effectively addressing the challenges of limited device memory. We implement On-device Sora on the iPhone 15 Pro, and the experimental evaluations demonstrate that it is capable of generating high-quality videos on the device, comparable to those produced by Open-Sora running on high-end GPUs. These results show that On-device Sora enables efficient and high-quality video generation on resource-constrained mobile devices, expanding accessibility, ensuring user privacy, reducing dependence on cloud infrastructure, and lowering associated costs. We envision the proposed On-device Sora as a significant first step toward democratizing state-of-the-art generative technologies, enabling video generation capabilities on commodity mobile and embedded devices. The code implementation is publicly available at an GitHub repository: https://github.com/eai-lab/On-device-Sora.

Scalable MatMul-free Language Modeling

Matrix multiplication (MatMul) typically dominates the overall computational cost of large language models (LLMs). This cost only grows as LLMs scale to larger embedding dimensions and context lengths. In this work, we show that MatMul operations can be completely eliminated from LLMs while maintaining strong performance at billion-parameter scales. Our experiments show that our proposed MatMul-free models achieve performance on-par with state-of-the-art Transformers that require far more memory during inference at a scale up to at least 2.7B parameters. We investigate the scaling laws and find that the performance gap between our MatMul-free models and full precision Transformers narrows as the model size increases. We also provide a GPU-efficient implementation of this model which reduces memory usage by up to 61% over an unoptimized baseline during training. By utilizing an optimized kernel during inference, our model's memory consumption can be reduced by more than 10x compared to unoptimized models. To properly quantify the efficiency of our architecture, we build a custom hardware solution on an FPGA which exploits lightweight operations beyond what GPUs are capable of. We processed billion-parameter scale models at 13W beyond human readable throughput, moving LLMs closer to brain-like efficiency. This work not only shows how far LLMs can be stripped back while still performing effectively, but also points at the types of operations future accelerators should be optimized for in processing the next generation of lightweight LLMs. Our code implementation is available at https://github.com/ridgerchu/matmulfreellm.

  • 8 authors
·
Jun 4, 2024

Context-aware Decoding Reduces Hallucination in Query-focused Summarization

Query-focused summarization (QFS) aims to provide a summary of a single document/multi documents that can satisfy the information needs of a given query. It is useful for various real-world applications, such as abstractive snippet generation or more recent retrieval augmented generation (RAG). A prototypical QFS pipeline consists of a retriever (sparse or dense retrieval) and a generator (usually a large language model). However, applying large language models (LLM) potentially leads to hallucinations, especially when the evidence contradicts the prior belief of LLMs. There has been growing interest in developing new decoding methods to improve generation quality and reduce hallucination. In this work, we conduct a large-scale reproducibility study on one recently proposed decoding method -- Context-aware Decoding (CAD). In addition to replicating CAD's experiments on news summarization datasets, we include experiments on QFS datasets, and conduct more rigorous analysis on computational complexity and hyperparameter sensitivity. Experiments with eight different language models show that performance-wise, CAD improves QFS quality by (1) reducing factuality errors/hallucinations while (2) mostly retaining the match of lexical patterns, measured by ROUGE scores, while also at a cost of increased inference-time FLOPs and reduced decoding speed. The code implementation based on Huggingface Library is made available https://github.com/zhichaoxu-shufe/context-aware-decoding-qfs

  • 1 authors
·
Dec 21, 2023

SpikeGPT: Generative Pre-trained Language Model with Spiking Neural Networks

As the size of large language models continue to scale, so does the computational resources required to run it. Spiking Neural Networks (SNNs) have emerged as an energy-efficient approach to deep learning that leverage sparse and event-driven activations to reduce the computational overhead associated with model inference. While they have become competitive with non-spiking models on many computer vision tasks, SNNs have also proven to be more challenging to train. As a result, their performance lags behind modern deep learning, and we are yet to see the effectiveness of SNNs in language generation. In this paper, inspired by the Receptance Weighted Key Value (RWKV) language model, we successfully implement `SpikeGPT', a generative language model with binary, event-driven spiking activation units. We train the proposed model on two model variants: 45M and 216M parameters. To the best of our knowledge, SpikeGPT is the largest backpropagation-trained SNN model to date, rendering it suitable for both the generation and comprehension of natural language. We achieve this by modifying the transformer block to replace multi-head self attention to reduce quadratic computational complexity O(N^2) to linear complexity O(N) with increasing sequence length. Input tokens are instead streamed in sequentially to our attention mechanism (as with typical SNNs). Our preliminary experiments show that SpikeGPT remains competitive with non-spiking models on tested benchmarks, while maintaining 20x fewer operations when processed on neuromorphic hardware that can leverage sparse, event-driven activations. Our code implementation is available at https://github.com/ridgerchu/SpikeGPT.

  • 4 authors
·
Feb 27, 2023

Glocal Information Bottleneck for Time Series Imputation

Time Series Imputation (TSI), which aims to recover missing values in temporal data, remains a fundamental challenge due to the complex and often high-rate missingness in real-world scenarios. Existing models typically optimize the point-wise reconstruction loss, focusing on recovering numerical values (local information). However, we observe that under high missing rates, these models still perform well in the training phase yet produce poor imputations and distorted latent representation distributions (global information) in the inference phase. This reveals a critical optimization dilemma: current objectives lack global guidance, leading models to overfit local noise and fail to capture global information of the data. To address this issue, we propose a new training paradigm, Glocal Information Bottleneck (Glocal-IB). Glocal-IB is model-agnostic and extends the standard IB framework by introducing a Global Alignment loss, derived from a tractable mutual information approximation. This loss aligns the latent representations of masked inputs with those of their originally observed counterparts. It helps the model retain global structure and local details while suppressing noise caused by missing values, giving rise to better generalization under high missingness. Extensive experiments on nine datasets confirm that Glocal-IB leads to consistently improved performance and aligned latent representations under missingness. Our code implementation is available in https://github.com/Muyiiiii/NeurIPS-25-Glocal-IB.

  • 5 authors
·
Oct 6 2

LightM-UNet: Mamba Assists in Lightweight UNet for Medical Image Segmentation

UNet and its variants have been widely used in medical image segmentation. However, these models, especially those based on Transformer architectures, pose challenges due to their large number of parameters and computational loads, making them unsuitable for mobile health applications. Recently, State Space Models (SSMs), exemplified by Mamba, have emerged as competitive alternatives to CNN and Transformer architectures. Building upon this, we employ Mamba as a lightweight substitute for CNN and Transformer within UNet, aiming at tackling challenges stemming from computational resource limitations in real medical settings. To this end, we introduce the Lightweight Mamba UNet (LightM-UNet) that integrates Mamba and UNet in a lightweight framework. Specifically, LightM-UNet leverages the Residual Vision Mamba Layer in a pure Mamba fashion to extract deep semantic features and model long-range spatial dependencies, with linear computational complexity. Extensive experiments conducted on two real-world 2D/3D datasets demonstrate that LightM-UNet surpasses existing state-of-the-art literature. Notably, when compared to the renowned nnU-Net, LightM-UNet achieves superior segmentation performance while drastically reducing parameter and computation costs by 116x and 21x, respectively. This highlights the potential of Mamba in facilitating model lightweighting. Our code implementation is publicly available at https://github.com/MrBlankness/LightM-UNet.

  • 6 authors
·
Mar 8, 2024

Generalizing to Unseen Domains in Diabetic Retinopathy with Disentangled Representations

Diabetic Retinopathy (DR), induced by diabetes, poses a significant risk of visual impairment. Accurate and effective grading of DR aids in the treatment of this condition. Yet existing models experience notable performance degradation on unseen domains due to domain shifts. Previous methods address this issue by simulating domain style through simple visual transformation and mitigating domain noise via learning robust representations. However, domain shifts encompass more than image styles. They overlook biases caused by implicit factors such as ethnicity, age, and diagnostic criteria. In our work, we propose a novel framework where representations of paired data from different domains are decoupled into semantic features and domain noise. The resulting augmented representation comprises original retinal semantics and domain noise from other domains, aiming to generate enhanced representations aligned with real-world clinical needs, incorporating rich information from diverse domains. Subsequently, to improve the robustness of the decoupled representations, class and domain prototypes are employed to interpolate the disentangled representations while data-aware weights are designed to focus on rare classes and domains. Finally, we devise a robust pixel-level semantic alignment loss to align retinal semantics decoupled from features, maintaining a balance between intra-class diversity and dense class features. Experimental results on multiple benchmarks demonstrate the effectiveness of our method on unseen domains. The code implementations are accessible on https://github.com/richard-peng-xia/DECO.

  • 9 authors
·
Jun 10, 2024

FLASK: Fine-grained Language Model Evaluation based on Alignment Skill Sets

Evaluation of Large Language Models (LLMs) is challenging because aligning to human values requires the composition of multiple skills and the required set of skills varies depending on the instruction. Recent studies have evaluated the performance of LLMs in two ways, (1) automatic evaluation on several independent benchmarks and (2) human or machined-based evaluation giving an overall score to the response. However, both settings are coarse-grained evaluations, not considering the nature of user instructions that require instance-wise skill composition, which limits the interpretation of the true capabilities of LLMs. In this paper, we introduce FLASK (Fine-grained Language Model Evaluation based on Alignment SKill Sets), a fine-grained evaluation protocol that can be used for both model-based and human-based evaluation which decomposes coarse-level scoring to an instance-wise skill set-level. Specifically, we define 12 fine-grained skills needed for LLMs to follow open-ended user instructions and construct an evaluation set by allocating a set of skills for each instance. Additionally, by annotating the target domains and difficulty level for each instance, FLASK provides a holistic view with a comprehensive analysis of a model's performance depending on skill, domain, and difficulty. Through using FLASK, we compare multiple open-sourced and proprietary LLMs and observe highly-correlated findings between model-based and human-based evaluations. FLASK enables developers to more accurately measure the model performance and how it can be improved by analyzing factors that make LLMs proficient in particular skills. For practitioners, FLASK can be used to recommend suitable models for particular situations through comprehensive comparison among various LLMs. We release the evaluation data and code implementation at https://github.com/kaistAI/FLASK.

  • 9 authors
·
Jul 20, 2023 2

Planning-Driven Programming: A Large Language Model Programming Workflow

The strong performance of large language models (LLMs) on natural language processing tasks raises extensive discussion on their application to code generation. Recent work suggests multiple sampling approaches to improve initial code generation accuracy or program repair approaches to refine the code. However, these methods suffer from LLMs' inefficiencies and limited reasoning capacity. In this work, we propose an LLM programming workflow (LPW) designed to improve both initial code generation and subsequent refinements within a structured two-phase workflow. Specifically, in the solution generation phase, the LLM first outlines a solution plan that decomposes the problem into manageable sub-problems and then verifies the generated solution plan through visible test cases. Subsequently, in the code implementation phase, the LLM initially drafts a code according to the solution plan and its verification. If the generated code fails the visible tests, the plan verification serves as the intended natural language solution to inform the refinement process for correcting bugs. We further introduce SLPW, a sampling variant of LPW, which initially generates multiple solution plans and plan verifications, produces a program for each plan and its verification, and refines each program as necessary until one successfully passes the visible tests. Compared to the state-of-the-art methods across various existing LLMs, our experimental results show that LPW significantly improves the Pass@1 accuracy by up to 16.4% on well-established text-to-code generation benchmarks, especially with a notable improvement of around 10% on challenging benchmarks. Additionally, SLPW demonstrates up to a 5.6% improvement over LPW and sets new state-of-the-art Pass@1 accuracy on various benchmarks, e.g., 98.2% on HumanEval, 84.8% on MBPP, 64.0% on APPS, and 35.3% on CodeContest, using GPT-4o as the backbone.

  • 4 authors
·
Nov 21, 2024

SciReplicate-Bench: Benchmarking LLMs in Agent-driven Algorithmic Reproduction from Research Papers

This study evaluates large language models (LLMs) in generating code from algorithm descriptions from recent NLP papers. The task requires two key competencies: (1) algorithm comprehension: synthesizing information from papers and academic literature to understand implementation logic, and (2) coding expertise: identifying dependencies and correctly implementing necessary APIs. To facilitate rigorous evaluation, we introduce SciReplicate-Bench, a benchmark of 100 tasks from 36 NLP papers published in 2024, featuring detailed annotations and comprehensive test cases. Building on SciReplicate-Bench, we propose Sci-Reproducer, a multi-agent framework consisting of a Paper Agent that interprets algorithmic concepts from literature and a Code Agent that retrieves dependencies from repositories and implement solutions. To assess algorithm understanding, we introduce reasoning graph accuracy, which quantifies similarity between generated and reference reasoning graphs derived from code comments and structure. For evaluating implementation quality, we employ execution accuracy, CodeBLEU, and repository dependency/API recall metrics. In our experiments, we evaluate various powerful Non-Reasoning LLMs and Reasoning LLMs as foundational models. The best-performing LLM using Sci-Reproducer achieves only 39% execution accuracy, highlighting the benchmark's difficulty.Our analysis identifies missing or inconsistent algorithm descriptions as key barriers to successful reproduction. We will open-source our benchmark, and code at https://github.com/xyzCS/SciReplicate-Bench.

  • 5 authors
·
Mar 31

Increasing LLM Coding Capabilities through Diverse Synthetic Coding Tasks

Large language models (LLMs) have shown impressive promise in code generation, yet their progress remains limited by the shortage of large-scale datasets that are both diverse and well-aligned with human reasoning. Most existing resources pair problems with solutions, but omit the intermediate thought process that guides coding. To close this gap, we present a scalable synthetic data generation pipeline that produces nearly 800k instruction-reasoning-code-test quadruplets. Each sample combines a task, a step-by-step reasoning trace, a working solution, and executable tests, enabling models to learn not just the what but also the how of problem solving. Our pipeline combines four key components: curated contest problems, web-mined content filtered by relevance classifiers, data expansion guided by reasoning patterns, and multi-stage execution-based validation. A genetic mutation algorithm further increases task diversity while maintaining consistency between reasoning traces and code implementations. Our key finding is that fine-tuning LLMs on this dataset yields consistent improvements on coding benchmarks. Beyond raw accuracy, reasoning-aware data can substitute for model scaling, generalize across architectures, and outperform leading open-source alternatives under identical sample budgets. Our work establishes reasoning-centered synthetic data generation as an efficient approach for advancing coding capabilities in LLMs. We publish our dataset and generation pipeline to facilitate further research.

  • 4 authors
·
Oct 27

Hyperbolic Large Language Models

Large language models (LLMs) have achieved remarkable success and demonstrated superior performance across various tasks, including natural language processing (NLP), weather forecasting, biological protein folding, text generation, and solving mathematical problems. However, many real-world data exhibit highly non-Euclidean latent hierarchical anatomy, such as protein networks, transportation networks, financial networks, brain networks, and linguistic structures or syntactic trees in natural languages. Effectively learning intrinsic semantic entailment and hierarchical relationships from these raw, unstructured input data using LLMs remains an underexplored area. Due to its effectiveness in modeling tree-like hierarchical structures, hyperbolic geometry -- a non-Euclidean space -- has rapidly gained popularity as an expressive latent representation space for complex data modeling across domains such as graphs, images, languages, and multi-modal data. Here, we provide a comprehensive and contextual exposition of recent advancements in LLMs that leverage hyperbolic geometry as a representation space to enhance semantic representation learning and multi-scale reasoning. Specifically, the paper presents a taxonomy of the principal techniques of Hyperbolic LLMs (HypLLMs) in terms of four main categories: (1) hyperbolic LLMs through exp/log maps; (2) hyperbolic fine-tuned models; (3) fully hyperbolic LLMs, and (4) hyperbolic state-space models. We also explore crucial potential applications and outline future research directions. A repository of key papers, models, datasets, and code implementations is available at https://github.com/sarangp2402/Hyperbolic-LLM-Models/tree/main.

  • 5 authors
·
Sep 6

Open-source Flux Transport (OFT). I. HipFT -- High-performance Flux Transport

Global solar photospheric magnetic maps play a critical role in solar and heliospheric physics research. Routine magnetograph measurements of the field occur only along the Sun-Earth line, leaving the far-side of the Sun unobserved. Surface Flux Transport (SFT) models attempt to mitigate this by modeling the surface evolution of the field. While such models have long been established in the community (with several releasing public full-Sun maps), none are open source. The Open Source Flux Transport (OFT) model seeks to fill this gap by providing an open and user-extensible SFT model that also builds on the knowledge of previous models with updated numerical and data acquisition/assimilation methods along with additional user-defined features. In this first of a series of papers on OFT, we introduce its computational core: the High-performance Flux Transport (HipFT) code (github.com/predsci/hipft). HipFT implements advection, diffusion, and data assimilation in a modular design that supports a variety of flow models and options. It can compute multiple realizations in a single run across model parameters to create ensembles of maps for uncertainty quantification and is high-performance through the use of multi-CPU and multi-GPU parallelism. HipFT is designed to enable users to easily write extensions, enhancing its flexibility and adaptability. We describe HipFT's model features, validations of its numerical methods, performance of its parallel and GPU-accelerated code implementation, analysis/post-processing options, and example use cases.

  • 8 authors
·
Jan 10

Design2Code: How Far Are We From Automating Front-End Engineering?

Generative AI has made rapid advancements in recent years, achieving unprecedented capabilities in multimodal understanding and code generation. This can enable a new paradigm of front-end development, in which multimodal LLMs might directly convert visual designs into code implementations. In this work, we formalize this as a Design2Code task and conduct comprehensive benchmarking. Specifically, we manually curate a benchmark of 484 diverse real-world webpages as test cases and develop a set of automatic evaluation metrics to assess how well current multimodal LLMs can generate the code implementations that directly render into the given reference webpages, given the screenshots as input. We also complement automatic metrics with comprehensive human evaluations. We develop a suite of multimodal prompting methods and show their effectiveness on GPT-4V and Gemini Pro Vision. We further finetune an open-source Design2Code-18B model that successfully matches the performance of Gemini Pro Vision. Both human evaluation and automatic metrics show that GPT-4V performs the best on this task compared to other models. Moreover, annotators think GPT-4V generated webpages can replace the original reference webpages in 49% of cases in terms of visual appearance and content; and perhaps surprisingly, in 64% of cases GPT-4V generated webpages are considered better than the original reference webpages. Our fine-grained break-down metrics indicate that open-source models mostly lag in recalling visual elements from the input webpages and in generating correct layout designs, while aspects like text content and coloring can be drastically improved with proper finetuning.

  • 5 authors
·
Mar 5, 2024 2

A Survey of Large Language Models for Healthcare: from Data, Technology, and Applications to Accountability and Ethics

The utilization of large language models (LLMs) in the Healthcare domain has generated both excitement and concern due to their ability to effectively respond to freetext queries with certain professional knowledge. This survey outlines the capabilities of the currently developed LLMs for Healthcare and explicates their development process, with the aim of providing an overview of the development roadmap from traditional Pretrained Language Models (PLMs) to LLMs. Specifically, we first explore the potential of LLMs to enhance the efficiency and effectiveness of various Healthcare applications highlighting both the strengths and limitations. Secondly, we conduct a comparison between the previous PLMs and the latest LLMs, as well as comparing various LLMs with each other. Then we summarize related Healthcare training data, training methods, optimization strategies, and usage. Finally, the unique concerns associated with deploying LLMs in Healthcare settings are investigated, particularly regarding fairness, accountability, transparency and ethics. Our survey provide a comprehensive investigation from perspectives of both computer science and Healthcare specialty. Besides the discussion about Healthcare concerns, we supports the computer science community by compiling a collection of open source resources, such as accessible datasets, the latest methodologies, code implementations, and evaluation benchmarks in the Github. Summarily, we contend that a significant paradigm shift is underway, transitioning from PLMs to LLMs. This shift encompasses a move from discriminative AI approaches to generative AI approaches, as well as a shift from model-centered methodologies to datacentered methodologies.

  • 7 authors
·
Oct 9, 2023 1

Visual Programmability: A Guide for Code-as-Thought in Chart Understanding

Chart understanding presents a critical test to the reasoning capabilities of Vision-Language Models (VLMs). Prior approaches face critical limitations: some rely on external tools, making them brittle and constrained by a predefined toolkit, while others fine-tune specialist models that often adopt a single reasoning strategy, such as text-based chain-of-thought (CoT). The intermediate steps of text-based reasoning are difficult to verify, which complicates the use of reinforcement-learning signals that reward factual accuracy. To address this, we propose a Code-as-Thought (CaT) approach to represent the visual information of a chart in a verifiable, symbolic format. Our key insight is that this strategy must be adaptive: a fixed, code-only implementation consistently fails on complex charts where symbolic representation is unsuitable. This finding leads us to introduce Visual Programmability: a learnable property that determines if a chart-question pair is better solved with code or direct visual analysis. We implement this concept in an adaptive framework where a VLM learns to choose between the CaT pathway and a direct visual reasoning pathway. The selection policy of the model is trained with reinforcement learning using a novel dual-reward system. This system combines a data-accuracy reward to ground the model in facts and prevent numerical hallucination, with a decision reward that teaches the model when to use each strategy, preventing it from defaulting to a single reasoning mode. Experiments demonstrate strong and robust performance across diverse chart-understanding benchmarks. Our work shows that VLMs can be taught not only to reason but also how to reason, dynamically selecting the optimal reasoning pathway for each task.

  • 9 authors
·
Sep 11 2

CODESYNC: Synchronizing Large Language Models with Dynamic Code Evolution at Scale

Large Language Models (LLMs) have exhibited exceptional performance in software engineering yet face challenges in adapting to continually evolving code knowledge, particularly regarding the frequent updates of third-party library APIs. This limitation, stemming from static pre-training datasets, often results in non-executable code or implementations with suboptimal safety and efficiency. To this end, this paper introduces CODESYNC, a data engine for identifying outdated code patterns and collecting real-time code knowledge updates from Python third-party libraries. Building upon CODESYNC, we develop CODESYNCBENCH, a comprehensive benchmark for assessing LLMs' ability to stay synchronized with code evolution, which covers real-world updates for 220 APIs from six Python libraries. Our benchmark offers 3,300 test cases across three evaluation tasks and an update-aware instruction tuning dataset consisting of 2,200 training samples. Extensive experiments on 14 state-of-the-art LLMs reveal that they struggle with dynamic code evolution, even with the support of advanced knowledge updating methods (e.g., DPO, ORPO, and SimPO). We believe that our benchmark can offer a strong foundation for the development of more effective methods for real-time code knowledge updating in the future. The experimental code and dataset are publicly available at: https://github.com/Lucky-voyage/Code-Sync.

  • 9 authors
·
Feb 23 2

Grokking Tickets: Lottery Tickets Accelerate Grokking

Grokking is one of the most surprising puzzles in neural network generalization: a network first reaches a memorization solution with perfect training accuracy and poor generalization, but with further training, it reaches a perfectly generalized solution. We aim to analyze the mechanism of grokking from the lottery ticket hypothesis, identifying the process to find the lottery tickets (good sparse subnetworks) as the key to describing the transitional phase between memorization and generalization. We refer to these subnetworks as ''Grokking tickets'', which is identified via magnitude pruning after perfect generalization. First, using ''Grokking tickets'', we show that the lottery tickets drastically accelerate grokking compared to the dense networks on various configurations (MLP and Transformer, and an arithmetic and image classification tasks). Additionally, to verify that ''Grokking ticket'' are a more critical factor than weight norms, we compared the ''good'' subnetworks with a dense network having the same L1 and L2 norms. Results show that the subnetworks generalize faster than the controlled dense model. In further investigations, we discovered that at an appropriate pruning rate, grokking can be achieved even without weight decay. We also show that speedup does not happen when using tickets identified at the memorization solution or transition between memorization and generalization or when pruning networks at the initialization (Random pruning, Grasp, SNIP, and Synflow). The results indicate that the weight norm of network parameters is not enough to explain the process of grokking, but the importance of finding good subnetworks to describe the transition from memorization to generalization. The implementation code can be accessed via this link: https://github.com/gouki510/Grokking-Tickets.

  • 3 authors
·
Oct 30, 2023

Efficient Reasoning via Reward Model

Reinforcement learning with verifiable rewards (RLVR) has been shown to enhance the reasoning capabilities of large language models (LLMs), enabling the development of large reasoning models (LRMs). However, LRMs such as DeepSeek-R1 and OpenAI o1 often generate verbose responses containing redundant or irrelevant reasoning step-a phenomenon known as overthinking-which substantially increases computational costs. Prior efforts to mitigate this issue commonly incorporate length penalties into the reward function, but we find they frequently suffer from two critical issues: length collapse and training collapse, resulting in sub-optimal performance. To address them, we propose a pipeline for training a Conciseness Reward Model (CRM) that scores the conciseness of reasoning path. Additionally, we introduce a novel reward formulation named Conciseness Reward Function (CRF) with explicit dependency between the outcome reward and conciseness score, thereby fostering both more effective and more efficient reasoning. From a theoretical standpoint, we demonstrate the superiority of the new reward from the perspective of variance reduction and improved convergence properties. Besides, on the practical side, extensive experiments on five mathematical benchmark datasets demonstrate the method's effectiveness and token efficiency, which achieves an 8.1% accuracy improvement and a 19.9% reduction in response token length on Qwen2.5-7B. Furthermore, the method generalizes well to other LLMs including Llama and Mistral. The implementation code and datasets are publicly available for reproduction: https://anonymous.4open.science/r/CRM.

  • 7 authors
·
Nov 12

Unsupervised Representation Learning for 3D Mesh Parameterization with Semantic and Visibility Objectives

Recent 3D generative models produce high-quality textures for 3D mesh objects. However, they commonly rely on the heavy assumption that input 3D meshes are accompanied by manual mesh parameterization (UV mapping), a manual task that requires both technical precision and artistic judgment. Industry surveys show that this process often accounts for a significant share of asset creation, creating a major bottleneck for 3D content creators. Moreover, existing automatic methods often ignore two perceptually important criteria: (1) semantic awareness (UV charts should align semantically similar 3D parts across shapes) and (2) visibility awareness (cutting seams should lie in regions unlikely to be seen). To overcome these shortcomings and to automate the mesh parameterization process, we present an unsupervised differentiable framework that augments standard geometry-preserving UV learning with semantic- and visibility-aware objectives. For semantic-awareness, our pipeline (i) segments the mesh into semantic 3D parts, (ii) applies an unsupervised learned per-part UV-parameterization backbone, and (iii) aggregates per-part charts into a unified UV atlas. For visibility-awareness, we use ambient occlusion (AO) as an exposure proxy and back-propagate a soft differentiable AO-weighted seam objective to steer cutting seams toward occluded regions. By conducting qualitative and quantitative evaluations against state-of-the-art methods, we show that the proposed method produces UV atlases that better support texture generation and reduce perceptible seam artifacts compared to recent baselines. Our implementation code is publicly available at: https://github.com/AHHHZ975/Semantic-Visibility-UV-Param.

  • 3 authors
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Sep 29

Scene4U: Hierarchical Layered 3D Scene Reconstruction from Single Panoramic Image for Your Immerse Exploration

The reconstruction of immersive and realistic 3D scenes holds significant practical importance in various fields of computer vision and computer graphics. Typically, immersive and realistic scenes should be free from obstructions by dynamic objects, maintain global texture consistency, and allow for unrestricted exploration. The current mainstream methods for image-driven scene construction involves iteratively refining the initial image using a moving virtual camera to generate the scene. However, previous methods struggle with visual discontinuities due to global texture inconsistencies under varying camera poses, and they frequently exhibit scene voids caused by foreground-background occlusions. To this end, we propose a novel layered 3D scene reconstruction framework from panoramic image, named Scene4U. Specifically, Scene4U integrates an open-vocabulary segmentation model with a large language model to decompose a real panorama into multiple layers. Then, we employs a layered repair module based on diffusion model to restore occluded regions using visual cues and depth information, generating a hierarchical representation of the scene. The multi-layer panorama is then initialized as a 3D Gaussian Splatting representation, followed by layered optimization, which ultimately produces an immersive 3D scene with semantic and structural consistency that supports free exploration. Scene4U outperforms state-of-the-art method, improving by 24.24% in LPIPS and 24.40% in BRISQUE, while also achieving the fastest training speed. Additionally, to demonstrate the robustness of Scene4U and allow users to experience immersive scenes from various landmarks, we build WorldVista3D dataset for 3D scene reconstruction, which contains panoramic images of globally renowned sites. The implementation code and dataset will be released at https://github.com/LongHZ140516/Scene4U .

  • 7 authors
·
Mar 31

Towards Label-Efficient Human Matting: A Simple Baseline for Weakly Semi-Supervised Trimap-Free Human Matting

This paper presents a new practical training method for human matting, which demands delicate pixel-level human region identification and significantly laborious annotations. To reduce the annotation cost, most existing matting approaches often rely on image synthesis to augment the dataset. However, the unnaturalness of synthesized training images brings in a new domain generalization challenge for natural images. To address this challenge, we introduce a new learning paradigm, weakly semi-supervised human matting (WSSHM), which leverages a small amount of expensive matte labels and a large amount of budget-friendly segmentation labels, to save the annotation cost and resolve the domain generalization problem. To achieve the goal of WSSHM, we propose a simple and effective training method, named Matte Label Blending (MLB), that selectively guides only the beneficial knowledge of the segmentation and matte data to the matting model. Extensive experiments with our detailed analysis demonstrate our method can substantially improve the robustness of the matting model using a few matte data and numerous segmentation data. Our training method is also easily applicable to real-time models, achieving competitive accuracy with breakneck inference speed (328 FPS on NVIDIA V100 GPU). The implementation code is available at https://github.com/clovaai/WSSHM.

  • 5 authors
·
Apr 1, 2024

Three-stage binarization of color document images based on discrete wavelet transform and generative adversarial networks

The efficient extraction of text information from the background in degraded color document images is an important challenge in the preservation of ancient manuscripts. The imperfect preservation of ancient manuscripts has led to different types of degradation over time, such as page yellowing, staining, and ink bleeding, seriously affecting the results of document image binarization. This work proposes an effective three-stage network method to image enhancement and binarization of degraded documents using generative adversarial networks (GANs). Specifically, in Stage-1, we first split the input images into multiple patches, and then split these patches into four single-channel patch images (gray, red, green, and blue). Then, three single-channel patch images (red, green, and blue) are processed by the discrete wavelet transform (DWT) with normalization. In Stage-2, we use four independent generators to separately train GAN models based on the four channels on the processed patch images to extract color foreground information. Finally, in Stage-3, we train two independent GAN models on the outputs of Stage-2 and the resized original input images (512x512) as the local and global predictions to obtain the final outputs. The experimental results show that the Avg-Score metrics of the proposed method are 77.64, 77.95, 79.05, 76.38, 75.34, and 77.00 on the (H)-DIBCO 2011, 2013, 2014, 2016, 2017, and 2018 datasets, which are at the state-of-the-art level. The implementation code for this work is available at https://github.com/abcpp12383/ThreeStageBinarization.

  • 6 authors
·
Nov 29, 2022

Entropy-Guided Attention for Private LLMs

The pervasiveness of proprietary language models has raised critical privacy concerns, necessitating advancements in private inference (PI), where computations are performed directly on encrypted data without revealing users' sensitive information. While PI offers a promising solution, its practical deployment is hindered by substantial communication and latency overheads, primarily stemming from nonlinear operations. To address this, we introduce an information-theoretic framework to characterize the role of nonlinearities in decoder-only language models, laying a principled foundation for optimizing transformer-architectures tailored to the demands of PI. By leveraging Shannon's entropy as a quantitative measure, we uncover the previously unexplored dual significance of nonlinearities: beyond ensuring training stability, they are crucial for maintaining attention head diversity. Specifically, we find that their removal triggers two critical failure modes: {\em entropy collapse} in deeper layers that destabilizes training, and {\em entropic overload} in earlier layers that leads to under-utilization of Multi-Head Attention's (MHA) representational capacity. We propose an entropy-guided attention mechanism paired with a novel entropy regularization technique to mitigate entropic overload. Additionally, we explore PI-friendly alternatives to layer normalization for preventing entropy collapse and stabilizing the training of LLMs with reduced-nonlinearities. Our study bridges the gap between information theory and architectural design, establishing entropy dynamics as a principled guide for developing efficient PI architectures. The code and implementation are available at https://github.com/Nandan91/entropy-guided-attention-llm{entropy-guided-llm}.

  • 2 authors
·
Jan 6 8

Enhancing Retrieval-Augmented Generation: A Study of Best Practices

Retrieval-Augmented Generation (RAG) systems have recently shown remarkable advancements by integrating retrieval mechanisms into language models, enhancing their ability to produce more accurate and contextually relevant responses. However, the influence of various components and configurations within RAG systems remains underexplored. A comprehensive understanding of these elements is essential for tailoring RAG systems to complex retrieval tasks and ensuring optimal performance across diverse applications. In this paper, we develop several advanced RAG system designs that incorporate query expansion, various novel retrieval strategies, and a novel Contrastive In-Context Learning RAG. Our study systematically investigates key factors, including language model size, prompt design, document chunk size, knowledge base size, retrieval stride, query expansion techniques, Contrastive In-Context Learning knowledge bases, multilingual knowledge bases, and Focus Mode retrieving relevant context at sentence-level. Through extensive experimentation, we provide a detailed analysis of how these factors influence response quality. Our findings offer actionable insights for developing RAG systems, striking a balance between contextual richness and retrieval-generation efficiency, thereby paving the way for more adaptable and high-performing RAG frameworks in diverse real-world scenarios. Our code and implementation details are publicly available.

  • 4 authors
·
Jan 13

Adapt then Unlearn: Exploring Parameter Space Semantics for Unlearning in Generative Adversarial Networks

Owing to the growing concerns about privacy and regulatory compliance, it is desirable to regulate the output of generative models. To that end, the objective of this work is to prevent the generation of outputs containing undesired features from a pre-trained Generative Adversarial Network (GAN) where the underlying training data set is inaccessible. Our approach is inspired by the observation that the parameter space of GANs exhibits meaningful directions that can be leveraged to suppress specific undesired features. However, such directions usually result in the degradation of the quality of generated samples. Our proposed two-stage method, known as 'Adapt-then-Unlearn,' excels at unlearning such undesirable features while also maintaining the quality of generated samples. In the initial stage, we adapt a pre-trained GAN on a set of negative samples (containing undesired features) provided by the user. Subsequently, we train the original pre-trained GAN using positive samples, along with a repulsion regularizer. This regularizer encourages the learned model parameters to move away from the parameters of the adapted model (first stage) while not degrading the generation quality. We provide theoretical insights into the proposed method. To the best of our knowledge, our approach stands as the first method addressing unlearning within the realm of high-fidelity GANs (such as StyleGAN). We validate the effectiveness of our method through comprehensive experiments, encompassing both class-level unlearning on the MNIST and AFHQ dataset and feature-level unlearning tasks on the CelebA-HQ dataset. Our code and implementation is available at: https://github.com/atriguha/Adapt_Unlearn.

  • 4 authors
·
Sep 25, 2023

Kolmogorov-Arnold Attention: Is Learnable Attention Better For Vision Transformers?

Kolmogorov-Arnold networks (KANs) are a remarkable innovation consisting of learnable activation functions with the potential to capture more complex relationships from data. Although KANs are useful in finding symbolic representations and continual learning of one-dimensional functions, their effectiveness in diverse machine learning (ML) tasks, such as vision, remains questionable. Presently, KANs are deployed by replacing multilayer perceptrons (MLPs) in deep network architectures, including advanced architectures such as vision Transformers (ViTs). In this paper, we are the first to design a general learnable Kolmogorov-Arnold Attention (KArAt) for vanilla ViTs that can operate on any choice of basis. However, the computing and memory costs of training them motivated us to propose a more modular version, and we designed particular learnable attention, called Fourier-KArAt. Fourier-KArAt and its variants either outperform their ViT counterparts or show comparable performance on CIFAR-10, CIFAR-100, and ImageNet-1K datasets. We dissect these architectures' performance and generalization capacity by analyzing their loss landscapes, weight distributions, optimizer path, attention visualization, and spectral behavior, and contrast them with vanilla ViTs. The goal of this paper is not to produce parameter- and compute-efficient attention, but to encourage the community to explore KANs in conjunction with more advanced architectures that require a careful understanding of learnable activations. Our open-source code and implementation details are available on: https://subhajitmaity.me/KArAt

  • 4 authors
·
Mar 13 3

OBoW: Online Bag-of-Visual-Words Generation for Self-Supervised Learning

Learning image representations without human supervision is an important and active research field. Several recent approaches have successfully leveraged the idea of making such a representation invariant under different types of perturbations, especially via contrastive-based instance discrimination training. Although effective visual representations should indeed exhibit such invariances, there are other important characteristics, such as encoding contextual reasoning skills, for which alternative reconstruction-based approaches might be better suited. With this in mind, we propose a teacher-student scheme to learn representations by training a convolutional net to reconstruct a bag-of-visual-words (BoW) representation of an image, given as input a perturbed version of that same image. Our strategy performs an online training of both the teacher network (whose role is to generate the BoW targets) and the student network (whose role is to learn representations), along with an online update of the visual-words vocabulary (used for the BoW targets). This idea effectively enables fully online BoW-guided unsupervised learning. Extensive experiments demonstrate the interest of our BoW-based strategy which surpasses previous state-of-the-art methods (including contrastive-based ones) in several applications. For instance, in downstream tasks such Pascal object detection, Pascal classification and Places205 classification, our method improves over all prior unsupervised approaches, thus establishing new state-of-the-art results that are also significantly better even than those of supervised pre-training. We provide the implementation code at https://github.com/valeoai/obow.

  • 6 authors
·
Dec 21, 2020

Discovering Influential Neuron Path in Vision Transformers

Vision Transformer models exhibit immense power yet remain opaque to human understanding, posing challenges and risks for practical applications. While prior research has attempted to demystify these models through input attribution and neuron role analysis, there's been a notable gap in considering layer-level information and the holistic path of information flow across layers. In this paper, we investigate the significance of influential neuron paths within vision Transformers, which is a path of neurons from the model input to output that impacts the model inference most significantly. We first propose a joint influence measure to assess the contribution of a set of neurons to the model outcome. And we further provide a layer-progressive neuron locating approach that efficiently selects the most influential neuron at each layer trying to discover the crucial neuron path from input to output within the target model. Our experiments demonstrate the superiority of our method finding the most influential neuron path along which the information flows, over the existing baseline solutions. Additionally, the neuron paths have illustrated that vision Transformers exhibit some specific inner working mechanism for processing the visual information within the same image category. We further analyze the key effects of these neurons on the image classification task, showcasing that the found neuron paths have already preserved the model capability on downstream tasks, which may also shed some lights on real-world applications like model pruning. The project website including implementation code is available at https://foundation-model-research.github.io/NeuronPath/.

  • 8 authors
·
Mar 12 2

DKDS: A Benchmark Dataset of Degraded Kuzushiji Documents with Seals for Detection and Binarization

Kuzushiji, a pre-modern Japanese cursive script, can currently be read and understood by only a few thousand trained experts in Japan. With the rapid development of deep learning, researchers have begun applying Optical Character Recognition (OCR) techniques to transcribe Kuzushiji into modern Japanese. Although existing OCR methods perform well on clean pre-modern Japanese documents written in Kuzushiji, they often fail to consider various types of noise, such as document degradation and seals, which significantly affect recognition accuracy. To the best of our knowledge, no existing dataset specifically addresses these challenges. To address this gap, we introduce the Degraded Kuzushiji Documents with Seals (DKDS) dataset as a new benchmark for related tasks. We describe the dataset construction process, which required the assistance of a trained Kuzushiji expert, and define two benchmark tracks: (1) text and seal detection and (2) document binarization. For the text and seal detection track, we provide baseline results using multiple versions of the You Only Look Once (YOLO) models for detecting Kuzushiji characters and seals. For the document binarization track, we present baseline results from traditional binarization algorithms, traditional algorithms combined with K-means clustering, and Generative Adversarial Network (GAN)-based methods. The DKDS dataset and the implementation code for baseline methods are available at https://ruiyangju.github.io/DKDS.

  • 4 authors
·
Nov 12

TextBraTS: Text-Guided Volumetric Brain Tumor Segmentation with Innovative Dataset Development and Fusion Module Exploration

Deep learning has demonstrated remarkable success in medical image segmentation and computer-aided diagnosis. In particular, numerous advanced methods have achieved state-of-the-art performance in brain tumor segmentation from MRI scans. While recent studies in other medical imaging domains have revealed that integrating textual reports with visual data can enhance segmentation accuracy, the field of brain tumor analysis lacks a comprehensive dataset that combines radiological images with corresponding textual annotations. This limitation has hindered the exploration of multimodal approaches that leverage both imaging and textual data. To bridge this critical gap, we introduce the TextBraTS dataset, the first publicly available volume-level multimodal dataset that contains paired MRI volumes and rich textual annotations, derived from the widely adopted BraTS2020 benchmark. Building upon this novel dataset, we propose a novel baseline framework and sequential cross-attention method for text-guided volumetric medical image segmentation. Through extensive experiments with various text-image fusion strategies and templated text formulations, our approach demonstrates significant improvements in brain tumor segmentation accuracy, offering valuable insights into effective multimodal integration techniques. Our dataset, implementation code, and pre-trained models are publicly available at https://github.com/Jupitern52/TextBraTS.

  • 10 authors
·
Jun 20

Large Language Model Distilling Medication Recommendation Model

The recommendation of medication is a vital aspect of intelligent healthcare systems, as it involves prescribing the most suitable drugs based on a patient's specific health needs. Unfortunately, many sophisticated models currently in use tend to overlook the nuanced semantics of medical data, while only relying heavily on identities. Furthermore, these models face significant challenges in handling cases involving patients who are visiting the hospital for the first time, as they lack prior prescription histories to draw upon. To tackle these issues, we harness the powerful semantic comprehension and input-agnostic characteristics of Large Language Models (LLMs). Our research aims to transform existing medication recommendation methodologies using LLMs. In this paper, we introduce a novel approach called Large Language Model Distilling Medication Recommendation (LEADER). We begin by creating appropriate prompt templates that enable LLMs to suggest medications effectively. However, the straightforward integration of LLMs into recommender systems leads to an out-of-corpus issue specific to drugs. We handle it by adapting the LLMs with a novel output layer and a refined tuning loss function. Although LLM-based models exhibit remarkable capabilities, they are plagued by high computational costs during inference, which is impractical for the healthcare sector. To mitigate this, we have developed a feature-level knowledge distillation technique, which transfers the LLM's proficiency to a more compact model. Extensive experiments conducted on two real-world datasets, MIMIC-III and MIMIC-IV, demonstrate that our proposed model not only delivers effective results but also is efficient. To ease the reproducibility of our experiments, we release the implementation code online.

  • 7 authors
·
Feb 5, 2024

FullFront: Benchmarking MLLMs Across the Full Front-End Engineering Workflow

Front-end engineering involves a complex workflow where engineers conceptualize designs, translate them into code, and iteratively refine the implementation. While recent benchmarks primarily focus on converting visual designs to code, we present FullFront, a benchmark designed to evaluate Multimodal Large Language Models (MLLMs) across the full front-end development pipeline. FullFront assesses three fundamental tasks that map directly to the front-end engineering pipeline: Webpage Design (conceptualization phase), Webpage Perception QA (comprehension of visual organization and elements), and Webpage Code Generation (implementation phase). Unlike existing benchmarks that use either scraped websites with bloated code or oversimplified LLM-generated HTML, FullFront employs a novel, two-stage process to transform real-world webpages into clean, standardized HTML while maintaining diverse visual designs and avoiding copyright issues. Extensive testing of state-of-the-art MLLMs reveals significant limitations in page perception, code generation (particularly for image handling and layout), and interaction implementation. Our results quantitatively demonstrate performance disparities across models and tasks, and highlight a substantial gap between current MLLM capabilities and human expert performance in front-end engineering. The FullFront benchmark and code are available in https://github.com/Mikivishy/FullFront.

  • 5 authors
·
May 22 2

\texttt{simple-idealized-1d-nlse}: Pseudo-Spectral Solver for the 1D Nonlinear Schrödinger Equation

We present an open-source Python implementation of an idealized high-order pseudo-spectral solver for the one-dimensional nonlinear Schr\"odinger equation (NLSE). The solver combines Fourier spectral spatial discretization with an adaptive eighth-order Dormand-Prince time integration scheme to achieve machine-precision conservation of mass and near-perfect preservation of momentum and energy for smooth solutions. The implementation accurately reproduces fundamental NLSE phenomena including soliton collisions with analytically predicted phase shifts, Akhmediev breather dynamics, and the development of modulation instability from noisy initial conditions. Four canonical test cases validate the numerical scheme: single soliton propagation, two-soliton elastic collision, breather evolution, and noise-seeded modulation instability. The solver employs a 2/3 dealiasing rule with exponential filtering to prevent aliasing errors from the cubic nonlinearity. Statistical analysis using Shannon, R\'enyi, and Tsallis entropies quantifies the spatio-temporal complexity of solutions, while phase space representations reveal the underlying coherence structure. The implementation prioritizes code transparency and educational accessibility over computational performance, providing a valuable pedagogical tool for exploring nonlinear wave dynamics. Complete source code, documentation, and example configurations are freely available, enabling reproducible computational experiments across diverse physical contexts where the NLSE governs wave evolution, including nonlinear optics, Bose-Einstein condensates, and ocean surface waves.

  • 5 authors
·
Sep 6

Relevance Isn't All You Need: Scaling RAG Systems With Inference-Time Compute Via Multi-Criteria Reranking

Modern Large Language Model (LLM) systems typically rely on Retrieval Augmented Generation (RAG) which aims to gather context that is useful for response generation. These RAG systems typically optimize strictly towards retrieving context that is maximally relevant to the query. However, conventional theory suggests that retrieval systems which seek to maximize context relevance without any additional explicit criteria can create information bottlenecks. We reaffirm this finding in the modern age of LLM's by showing that in standard RAG pipelines, maximizing for context relevance alone can degrade downstream response quality. In response, we show evaluations of existing RAG methods which account for both context relevance and answer quality. These evaluations introduce a novel finding that existing RAG systems scale poorly with inference time compute usage when considering our combined metric. We introduce "RErank BEyond reLevance (REBEL)", which enables RAG systems to scale with inference-time compute via injection of multi-criteria optimization using Chain-of-Thought prompting (and optionally Multi-Turn dialogue). Ultimately, this enables a new performance/speed tradeoff curve, where RAG systems are able to achieve both higher relevance of retrieved contexts and superior answer quality as inference time increases. Code for the implementation of our method in llama-index can be found at the following PR: https://github.com/run-llama/llama_index/pull/17590. Code for running experiments using this llama-index implementation can be found at https://github.com/microsoft/REBEL.

  • 2 authors
·
Mar 13

What learning algorithm is in-context learning? Investigations with linear models

Neural sequence models, especially transformers, exhibit a remarkable capacity for in-context learning. They can construct new predictors from sequences of labeled examples (x, f(x)) presented in the input without further parameter updates. We investigate the hypothesis that transformer-based in-context learners implement standard learning algorithms implicitly, by encoding smaller models in their activations, and updating these implicit models as new examples appear in the context. Using linear regression as a prototypical problem, we offer three sources of evidence for this hypothesis. First, we prove by construction that transformers can implement learning algorithms for linear models based on gradient descent and closed-form ridge regression. Second, we show that trained in-context learners closely match the predictors computed by gradient descent, ridge regression, and exact least-squares regression, transitioning between different predictors as transformer depth and dataset noise vary, and converging to Bayesian estimators for large widths and depths. Third, we present preliminary evidence that in-context learners share algorithmic features with these predictors: learners' late layers non-linearly encode weight vectors and moment matrices. These results suggest that in-context learning is understandable in algorithmic terms, and that (at least in the linear case) learners may rediscover standard estimation algorithms. Code and reference implementations are released at https://github.com/ekinakyurek/google-research/blob/master/incontext.

  • 5 authors
·
Nov 28, 2022

Benchmarking Computational Methods for Emerging Drug-Drug Interaction Prediction

Motivation: Emerging drug-drug interaction (DDI) prediction is crucial for new drugs but is hindered by distribution changes between known and new drugs in real-world scenarios. Current evaluation often neglects these changes, relying on unrealistic i.i.d. split due to the absence of drug approval data. Results: We propose DDI-Ben, a benchmarking framework for emerging DDI prediction under distribution changes. DDI-Ben introduces a distribution change simulation framework that leverages distribution changes between drug sets as a surrogate for real-world distribution changes of DDIs, and is compatible with various drug split strategies. Through extensive benchmarking on ten representative methods, we show that most existing approaches suffer substantial performance degradation under distribution changes. Our analysis further indicates that large language model (LLM) based methods and the integration of drug-related textual information offer promising robustness against such degradation. To support future research, we release the benchmark datasets with simulated distribution changes. Overall, DDI-Ben highlights the importance of explicitly addressing distribution changes and provides a foundation for developing more resilient methods for emerging DDI prediction. Availability and implementation: Our code and data are available at https://github.com/LARS-research/DDI-Bench.

  • 4 authors
·
Oct 24, 2024

BioGraphFusion: Graph Knowledge Embedding for Biological Completion and Reasoning

Motivation: Biomedical knowledge graphs (KGs) are crucial for drug discovery and disease understanding, yet their completion and reasoning are challenging. Knowledge Embedding (KE) methods capture global semantics but struggle with dynamic structural integration, while Graph Neural Networks (GNNs) excel locally but often lack semantic understanding. Even ensemble approaches, including those leveraging language models, often fail to achieve a deep, adaptive, and synergistic co-evolution between semantic comprehension and structural learning. Addressing this critical gap in fostering continuous, reciprocal refinement between these two aspects in complex biomedical KGs is paramount. Results: We introduce BioGraphFusion, a novel framework for deeply synergistic semantic and structural learning. BioGraphFusion establishes a global semantic foundation via tensor decomposition, guiding an LSTM-driven mechanism to dynamically refine relation embeddings during graph propagation. This fosters adaptive interplay between semantic understanding and structural learning, further enhanced by query-guided subgraph construction and a hybrid scoring mechanism. Experiments across three key biomedical tasks demonstrate BioGraphFusion's superior performance over state-of-the-art KE, GNN, and ensemble models. A case study on Cutaneous Malignant Melanoma 1 (CMM1) highlights its ability to unveil biologically meaningful pathways. Availability and Implementation: Source code and all training data are freely available for download at https://github.com/Y-TARL/BioGraphFusion. Supplementary information: Supplementary data are available at Bioinformatics online.

  • 6 authors
·
Jul 19

NestedMorph: Enhancing Deformable Medical Image Registration with Nested Attention Mechanisms

Deformable image registration is crucial for aligning medical images in a non-linear fashion across different modalities, allowing for precise spatial correspondence between varying anatomical structures. This paper presents NestedMorph, a novel network utilizing a Nested Attention Fusion approach to improve intra-subject deformable registration between T1-weighted (T1w) MRI and diffusion MRI (dMRI) data. NestedMorph integrates high-resolution spatial details from an encoder with semantic information from a decoder using a multi-scale framework, enhancing both local and global feature extraction. Our model notably outperforms existing methods, including CNN-based approaches like VoxelMorph, MIDIR, and CycleMorph, as well as Transformer-based models such as TransMorph and ViT-V-Net, and traditional techniques like NiftyReg and SyN. Evaluations on the HCP dataset demonstrate that NestedMorph achieves superior performance across key metrics, including SSIM, HD95, and SDlogJ, with the highest SSIM of 0.89, and the lowest HD95 of 2.5 and SDlogJ of 0.22. These results highlight NestedMorph's ability to capture both local and global image features effectively, leading to superior registration performance. The promising outcomes of this study underscore NestedMorph's potential to significantly advance deformable medical image registration, providing a robust framework for future research and clinical applications. The source code and our implementation are available at: https://bit.ly/3zdVqcg

  • 3 authors
·
Oct 3, 2024

AceReason-Nemotron: Advancing Math and Code Reasoning through Reinforcement Learning

Despite recent progress in large-scale reinforcement learning (RL) for reasoning, the training recipe for building high-performing reasoning models remains elusive. Key implementation details of frontier models, such as DeepSeek-R1, including data curation strategies and RL training recipe, are often omitted. Moreover, recent research indicates distillation remains more effective than RL for smaller models. In this work, we demonstrate that large-scale RL can significantly enhance the reasoning capabilities of strong, small- and mid-sized models, achieving results that surpass those of state-of-the-art distillation-based models. We systematically study the RL training process through extensive ablations and propose a simple yet effective approach: first training on math-only prompts, then on code-only prompts. Notably, we find that math-only RL not only significantly enhances the performance of strong distilled models on math benchmarks (e.g., +14.6% / +17.2% on AIME 2025 for the 7B / 14B models), but also code reasoning tasks (e.g., +6.8% / +5.8% on LiveCodeBench for the 7B / 14B models). In addition, extended code-only RL iterations further improve performance on code benchmarks with minimal or no degradation in math results. We develop a robust data curation pipeline to collect challenging prompts with high-quality, verifiable answers and test cases to enable verification-based RL across both domains. Finally, we identify key experimental insights, including curriculum learning with progressively increasing response lengths and the stabilizing effect of on-policy parameter updates. We find that RL not only elicits the foundational reasoning capabilities acquired during pretraining and supervised fine-tuning (e.g., distillation), but also pushes the limits of the model's reasoning ability, enabling it to solve problems that were previously unsolvable.

  • 8 authors
·
May 22 2

ArzEn-LLM: Code-Switched Egyptian Arabic-English Translation and Speech Recognition Using LLMs

Motivated by the widespread increase in the phenomenon of code-switching between Egyptian Arabic and English in recent times, this paper explores the intricacies of machine translation (MT) and automatic speech recognition (ASR) systems, focusing on translating code-switched Egyptian Arabic-English to either English or Egyptian Arabic. Our goal is to present the methodologies employed in developing these systems, utilizing large language models such as LLama and Gemma. In the field of ASR, we explore the utilization of the Whisper model for code-switched Egyptian Arabic recognition, detailing our experimental procedures including data preprocessing and training techniques. Through the implementation of a consecutive speech-to-text translation system that integrates ASR with MT, we aim to overcome challenges posed by limited resources and the unique characteristics of the Egyptian Arabic dialect. Evaluation against established metrics showcases promising results, with our methodologies yielding a significant improvement of 56% in English translation over the state-of-the-art and 9.3% in Arabic translation. Since code-switching is deeply inherent in spoken languages, it is crucial that ASR systems can effectively handle this phenomenon. This capability is crucial for enabling seamless interaction in various domains, including business negotiations, cultural exchanges, and academic discourse. Our models and code are available as open-source resources. Code: http://github.com/ahmedheakl/arazn-llm}, Models: http://huggingface.co/collections/ahmedheakl/arazn-llm-662ceaf12777656607b9524e.

  • 5 authors
·
Jun 26, 2024 5

Large Action Models: From Inception to Implementation

As AI continues to advance, there is a growing demand for systems that go beyond language-based assistance and move toward intelligent agents capable of performing real-world actions. This evolution requires the transition from traditional Large Language Models (LLMs), which excel at generating textual responses, to Large Action Models (LAMs), designed for action generation and execution within dynamic environments. Enabled by agent systems, LAMs hold the potential to transform AI from passive language understanding to active task completion, marking a significant milestone in the progression toward artificial general intelligence. In this paper, we present a comprehensive framework for developing LAMs, offering a systematic approach to their creation, from inception to deployment. We begin with an overview of LAMs, highlighting their unique characteristics and delineating their differences from LLMs. Using a Windows OS-based agent as a case study, we provide a detailed, step-by-step guide on the key stages of LAM development, including data collection, model training, environment integration, grounding, and evaluation. This generalizable workflow can serve as a blueprint for creating functional LAMs in various application domains. We conclude by identifying the current limitations of LAMs and discussing directions for future research and industrial deployment, emphasizing the challenges and opportunities that lie ahead in realizing the full potential of LAMs in real-world applications. The code for the data collection process utilized in this paper is publicly available at: https://github.com/microsoft/UFO/tree/main/dataflow, and comprehensive documentation can be found at https://microsoft.github.io/UFO/dataflow/overview/.

  • 18 authors
·
Dec 13, 2024 5

Splatfacto-W: A Nerfstudio Implementation of Gaussian Splatting for Unconstrained Photo Collections

Novel view synthesis from unconstrained in-the-wild image collections remains a significant yet challenging task due to photometric variations and transient occluders that complicate accurate scene reconstruction. Previous methods have approached these issues by integrating per-image appearance features embeddings in Neural Radiance Fields (NeRFs). Although 3D Gaussian Splatting (3DGS) offers faster training and real-time rendering, adapting it for unconstrained image collections is non-trivial due to the substantially different architecture. In this paper, we introduce Splatfacto-W, an approach that integrates per-Gaussian neural color features and per-image appearance embeddings into the rasterization process, along with a spherical harmonics-based background model to represent varying photometric appearances and better depict backgrounds. Our key contributions include latent appearance modeling, efficient transient object handling, and precise background modeling. Splatfacto-W delivers high-quality, real-time novel view synthesis with improved scene consistency in in-the-wild scenarios. Our method improves the Peak Signal-to-Noise Ratio (PSNR) by an average of 5.3 dB compared to 3DGS, enhances training speed by 150 times compared to NeRF-based methods, and achieves a similar rendering speed to 3DGS. Additional video results and code integrated into Nerfstudio are available at https://kevinxu02.github.io/splatfactow/.

  • 3 authors
·
Jul 17, 2024 2

Flash Sparse Attention: An Alternative Efficient Implementation of Native Sparse Attention Kernel

Recent progress in sparse attention mechanisms has demonstrated strong potential for reducing the computational cost of long-context training and inference in large language models (LLMs). Native Sparse Attention (NSA), a state-of-the-art approach, introduces natively trainable, hardware-aligned sparse attention that delivers substantial system-level performance gains while maintaining accuracy comparable to full attention. However, the kernel implementation of NSA relies on a query-grouping strategy that is efficient only with large Grouped Query Attention (GQA) sizes, whereas modern LLMs typically adopt much smaller GQA groups, which limits the applicability of this sparse algorithmic advance. In this work, we propose Flash Sparse Attention (FSA), which includes an alternative kernel design that enables efficient NSA computation across a wide range of popular LLMs with varied smaller GQA group sizes on modern GPUs. Compared to vanilla NSA kernel implementation, our empirical evaluation demonstrates that FSA achieves (i) up to 3.5times and on average 1.6times kernel-level latency reduction, (ii) up to 1.25times and 1.09times on average end-to-end training speedup on state-of-the-art LLMs, and (iii) up to 1.36times and 1.11times on average end-to-end prefill speedup on state-of-the-art LLMs. The source code is open-sourced and publicly available at https://github.com/Relaxed-System-Lab/Flash-Sparse-Attention.

  • 3 authors
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Aug 25

Neural Circuit Diagrams: Robust Diagrams for the Communication, Implementation, and Analysis of Deep Learning Architectures

Diagrams matter. Unfortunately, the deep learning community has no standard method for diagramming architectures. The current combination of linear algebra notation and ad-hoc diagrams fails to offer the necessary precision to understand architectures in all their detail. However, this detail is critical for faithful implementation, mathematical analysis, further innovation, and ethical assurances. I present neural circuit diagrams, a graphical language tailored to the needs of communicating deep learning architectures. Neural circuit diagrams naturally keep track of the changing arrangement of data, precisely show how operations are broadcast over axes, and display the critical parallel behavior of linear operations. A lingering issue with existing diagramming methods is the inability to simultaneously express the detail of axes and the free arrangement of data, which neural circuit diagrams solve. Their compositional structure is analogous to code, creating a close correspondence between diagrams and implementation. In this work, I introduce neural circuit diagrams for an audience of machine learning researchers. After introducing neural circuit diagrams, I cover a host of architectures to show their utility and breed familiarity. This includes the transformer architecture, convolution (and its difficult-to-explain extensions), residual networks, the U-Net, and the vision transformer. I include a Jupyter notebook that provides evidence for the close correspondence between diagrams and code. Finally, I examine backpropagation using neural circuit diagrams. I show their utility in providing mathematical insight and analyzing algorithms' time and space complexities.

  • 1 authors
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Feb 8, 2024 1

FeatBench: Evaluating Coding Agents on Feature Implementation for Vibe Coding

The rapid advancement of Large Language Models (LLMs) has given rise to a novel software development paradigm known as "vibe coding," where users interact with coding agents through high-level natural language. However, existing evaluation benchmarks for code generation inadequately assess an agent's vibe coding capabilities. Existing benchmarks are misaligned, as they either require code-level specifications or focus narrowly on issue-solving, neglecting the critical scenario of feature implementation within the vibe coding paradiam. To address this gap, we propose FeatBench, a novel benchmark for vibe coding that focuses on feature implementation. Our benchmark is distinguished by several key features: 1. Pure Natural Language Prompts. Task inputs consist solely of abstract natural language descriptions, devoid of any code or structural hints. 2. A Rigorous & Evolving Data Collection Process. FeatBench is built on a multi-level filtering pipeline to ensure quality and a fully automated pipeline to evolve the benchmark, mitigating data contamination. 3. Comprehensive Test Cases. Each task includes Fail-to-Pass (F2P) and Pass-to-Pass (P2P) tests to verify correctness and prevent regressions. 4. Diverse Application Domains. The benchmark includes repositories from diverse domains to ensure it reflects real-world scenarios. We evaluate two state-of-the-art agent frameworks with four leading LLMs on FeatBench. Our evaluation reveals that feature implementation within the vibe coding paradigm is a significant challenge, with the highest success rate of only 29.94%. Our analysis also reveals a tendency for "aggressive implementation," a strategy that paradoxically leads to both critical failures and superior software design. We release FeatBench, our automated collection pipeline, and all experimental results to facilitate further community research.

  • 3 authors
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Sep 26

Code-Survey: An LLM-Driven Methodology for Analyzing Large-Scale Codebases

Modern software systems like the Linux kernel are among the world's largest and most intricate codebases, continually evolving with new features and increasing complexity. Understanding these systems poses significant challenges due to their scale and the unstructured nature of development artifacts such as commits and mailing list discussions. We introduce Code-Survey, the first LLM-driven methodology designed to systematically explore and analyze large-scale codebases. The central principle behind Code-Survey is to treat LLMs as human participants, acknowledging that software development is also a social activity and thereby enabling the application of established social science techniques. By carefully designing surveys, Code-Survey transforms unstructured data, such as commits, emails, into organized, structured, and analyzable datasets. This enables quantitative analysis of complex software evolution and uncovers valuable insights related to design, implementation, maintenance, reliability, and security. To demonstrate the effectiveness of Code-Survey, we apply it to the Linux kernel's eBPF subsystem. We construct the Linux-bpf dataset, comprising over 670 features and 16,000 commits from the Linux community. Our quantitative analysis uncovers important insights into the evolution of eBPF, such as development patterns, feature interdependencies, and areas requiring attention for reliability and security. The insights have been initially validated by eBPF experts. Furthermore, Code-Survey can be directly applied to other subsystems within Linux and to other large-scale software projects. By providing a versatile tool for systematic analysis, Code-Survey facilitates a deeper understanding of complex software systems, enabling improvements across a variety of domains and supporting a wide range of empirical studies. The code and dataset is open-sourced.

  • 4 authors
·
Sep 24, 2024

Where Are Large Language Models for Code Generation on GitHub?

The increasing use of Large Language Models (LLMs) in software development has garnered significant attention from researchers assessing the quality of the code they generate. However, much of the research focuses on controlled datasets such as HumanEval, which fail to adequately represent how developers actually utilize LLMs' code generation capabilities or clarify the characteristics of LLM-generated code in real-world development scenarios. To bridge this gap, our study investigates the characteristics of LLM-generated code and its corresponding projects hosted on GitHub. Our findings reveal several key insights: (1) ChatGPT and Copilot are the most frequently utilized for generating code on GitHub. In contrast, there is very little code generated by other LLMs on GitHub. (2) Projects containing ChatGPT/Copilot-generated code are often small and less known, led by individuals or small teams. Despite this, most projects are continuously evolving and improving. (3) ChatGPT/Copilot is mainly utilized for generating Python, Java, and TypeScript scripts for data processing and transformation. C/C++ and JavaScript code generation focuses on algorithm and data structure implementation and user interface code. Most ChatGPT/Copilot-generated code snippets are relatively short and exhibit low complexity. (4) Compared to human-written code, ChatGPT/Copilot-generated code exists in a small proportion of projects and generally undergoes fewer modifications. Additionally, modifications due to bugs are even fewer, ranging from just 3% to 8% across different languages. (5) Most comments on ChatGPT/Copilot-generated code lack detailed information, often only stating the code's origin without mentioning prompts, human modifications, or testing status. Based on these findings, we discuss the implications for researchers and practitioners.

  • 6 authors
·
Jun 27, 2024

On Learning Meaningful Code Changes via Neural Machine Translation

Recent years have seen the rise of Deep Learning (DL) techniques applied to source code. Researchers have exploited DL to automate several development and maintenance tasks, such as writing commit messages, generating comments and detecting vulnerabilities among others. One of the long lasting dreams of applying DL to source code is the possibility to automate non-trivial coding activities. While some steps in this direction have been taken (e.g., learning how to fix bugs), there is still a glaring lack of empirical evidence on the types of code changes that can be learned and automatically applied by DL. Our goal is to make this first important step by quantitatively and qualitatively investigating the ability of a Neural Machine Translation (NMT) model to learn how to automatically apply code changes implemented by developers during pull requests. We train and experiment with the NMT model on a set of 236k pairs of code components before and after the implementation of the changes provided in the pull requests. We show that, when applied in a narrow enough context (i.e., small/medium-sized pairs of methods before/after the pull request changes), NMT can automatically replicate the changes implemented by developers during pull requests in up to 36% of the cases. Moreover, our qualitative analysis shows that the model is capable of learning and replicating a wide variety of meaningful code changes, especially refactorings and bug-fixing activities. Our results pave the way for novel research in the area of DL on code, such as the automatic learning and applications of refactoring.

  • 5 authors
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Jan 25, 2019