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Dec 16

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

Production of Categorical Data Verifying Differential Privacy: Conception and Applications to Machine Learning

Private and public organizations regularly collect and analyze digitalized data about their associates, volunteers, clients, etc. However, because most personal data are sensitive, there is a key challenge in designing privacy-preserving systems. To tackle privacy concerns, research communities have proposed different methods to preserve privacy, with Differential privacy (DP) standing out as a formal definition that allows quantifying the privacy-utility trade-off. Besides, with the local DP (LDP) model, users can sanitize their data locally before transmitting it to the server. The objective of this thesis is thus two-fold: O_1) To improve the utility and privacy in multiple frequency estimates under LDP guarantees, which is fundamental to statistical learning. And O_2) To assess the privacy-utility trade-off of machine learning (ML) models trained over differentially private data. For O_1, we first tackled the problem from two "multiple" perspectives, i.e., multiple attributes and multiple collections throughout time, while focusing on utility. Secondly, we focused our attention on the multiple attributes aspect only, in which we proposed a solution focusing on privacy while preserving utility. In both cases, we demonstrate through analytical and experimental validations the advantages of our proposed solutions over state-of-the-art LDP protocols. For O_2, we empirically evaluated ML-based solutions designed to solve real-world problems while ensuring DP guarantees. Indeed, we mainly used the input data perturbation setting from the privacy-preserving ML literature. This is the situation in which the whole dataset is sanitized independently and, thus, we implemented LDP algorithms from the perspective of the centralized data owner. In all cases, we concluded that differentially private ML models achieve nearly the same utility metrics as non-private ones.

  • 1 authors
·
Apr 2, 2022

Distilling from Similar Tasks for Transfer Learning on a Budget

We address the challenge of getting efficient yet accurate recognition systems with limited labels. While recognition models improve with model size and amount of data, many specialized applications of computer vision have severe resource constraints both during training and inference. Transfer learning is an effective solution for training with few labels, however often at the expense of a computationally costly fine-tuning of large base models. We propose to mitigate this unpleasant trade-off between compute and accuracy via semi-supervised cross-domain distillation from a set of diverse source models. Initially, we show how to use task similarity metrics to select a single suitable source model to distill from, and that a good selection process is imperative for good downstream performance of a target model. We dub this approach DistillNearest. Though effective, DistillNearest assumes a single source model matches the target task, which is not always the case. To alleviate this, we propose a weighted multi-source distillation method to distill multiple source models trained on different domains weighted by their relevance for the target task into a single efficient model (named DistillWeighted). Our methods need no access to source data, and merely need features and pseudo-labels of the source models. When the goal is accurate recognition under computational constraints, both DistillNearest and DistillWeighted approaches outperform both transfer learning from strong ImageNet initializations as well as state-of-the-art semi-supervised techniques such as FixMatch. Averaged over 8 diverse target tasks our multi-source method outperforms the baselines by 5.6%-points and 4.5%-points, respectively.

  • 3 authors
·
Apr 24, 2023

POPri: Private Federated Learning using Preference-Optimized Synthetic Data

In practical settings, differentially private Federated learning (DP-FL) is the dominant method for training models from private, on-device client data. Recent work has suggested that DP-FL may be enhanced or outperformed by methods that use DP synthetic data (Wu et al., 2024; Hou et al., 2024). The primary algorithms for generating DP synthetic data for FL applications require careful prompt engineering based on public information and/or iterative private client feedback. Our key insight is that the private client feedback collected by prior DP synthetic data methods (Hou et al., 2024; Xie et al., 2024) can be viewed as an RL (reinforcement learning) reward. Our algorithm, Policy Optimization for Private Data (POPri) harnesses client feedback using policy optimization algorithms such as Direct Preference Optimization (DPO) to fine-tune LLMs to generate high-quality DP synthetic data. To evaluate POPri, we release LargeFedBench, a new federated text benchmark for uncontaminated LLM evaluations on federated client data. POPri substantially improves the utility of DP synthetic data relative to prior work on LargeFedBench datasets and an existing benchmark from Xie et al. (2024). POPri closes the gap between next-token prediction accuracy in the fully-private and non-private settings by up to 58%, compared to 28% for prior synthetic data methods, and 3% for state-of-the-art DP federated learning methods. The code and data are available at https://github.com/meiyuw/POPri.

  • 5 authors
·
Apr 23

Hydra: Structured Cross-Source Enhanced Large Language Model Reasoning

Retrieval-augmented generation (RAG) enhances large language models (LLMs) by incorporating external knowledge. Current hybrid RAG system retrieves evidence from both knowledge graphs (KGs) and text documents to support LLM reasoning. However, it faces challenges like handling multi-hop reasoning, multi-entity questions, multi-source verification, and effective graph utilization. To address these limitations, we present Hydra, a training-free framework that unifies graph topology, document semantics, and source reliability to support deep, faithful reasoning in LLMs. Hydra handles multi-hop and multi-entity problems through agent-driven exploration that combines structured and unstructured retrieval, increasing both diversity and precision of evidence. To tackle multi-source verification, Hydra uses a tri-factor cross-source verification (source trustworthiness assessment, cross-source corroboration, and entity-path alignment), to balance topic relevance with cross-modal agreement. By leveraging graph structure, Hydra fuses heterogeneous sources, guides efficient exploration, and prunes noise early. Comprehensive experiments on seven benchmark datasets show that Hydra achieves overall state-of-the-art results on all benchmarks with GPT-3.5, outperforming the strong hybrid baseline ToG-2 by an average of 20.3% and up to 30.1%. Furthermore, Hydra enables smaller models (e.g., Llama-3.1-8B) to achieve reasoning performance comparable to that of GPT-4-Turbo.

  • 7 authors
·
May 23

Curry-DPO: Enhancing Alignment using Curriculum Learning & Ranked Preferences

Direct Preference Optimization (DPO) is an effective technique that leverages pairwise preference data (usually one chosen and rejected response pair per user prompt) to align LLMs to human preferences. In practice, multiple responses can exist for a given prompt with varying quality relative to each other. With availability of such quality ratings for multiple responses, we propose utilizing these responses to create multiple preference pairs for a given prompt. Our work focuses on systematically using the constructed multiple preference pair in DPO training via curriculum learning methodology. In particular, we order these multiple pairs of preference data from easy to hard (emulating curriculum training) according to various criteria. We show detailed comparisons of our proposed approach to the standard single-pair DPO setting. Our method, which we call Curry-DPO consistently shows increased performance gains on MTbench, Vicuna, WizardLM, and the UltraFeedback test set, highlighting its effectiveness. More specifically, Curry-DPO achieves a score of 7.43 on MT-bench with Zephy-7B model outperforming majority of existing LLMs with similar parameter size. Curry-DPO also achieves the highest adjusted win rates on Vicuna, WizardLM, and UltraFeedback test datasets (90.7%, 87.1%, and 87.9% respectively) in our experiments, with notable gains of upto 7.5% when compared to standard DPO technique.

  • 5 authors
·
Mar 11, 2024

Phased DMD: Few-step Distribution Matching Distillation via Score Matching within Subintervals

Distribution Matching Distillation (DMD) distills score-based generative models into efficient one-step generators, without requiring a one-to-one correspondence with the sampling trajectories of their teachers. However, limited model capacity causes one-step distilled models underperform on complex generative tasks, e.g., synthesizing intricate object motions in text-to-video generation. Directly extending DMD to multi-step distillation increases memory usage and computational depth, leading to instability and reduced efficiency. While prior works propose stochastic gradient truncation as a potential solution, we observe that it substantially reduces the generation diversity of multi-step distilled models, bringing it down to the level of their one-step counterparts. To address these limitations, we propose Phased DMD, a multi-step distillation framework that bridges the idea of phase-wise distillation with Mixture-of-Experts (MoE), reducing learning difficulty while enhancing model capacity. Phased DMD is built upon two key ideas: progressive distribution matching and score matching within subintervals. First, our model divides the SNR range into subintervals, progressively refining the model to higher SNR levels, to better capture complex distributions. Next, to ensure the training objective within each subinterval is accurate, we have conducted rigorous mathematical derivations. We validate Phased DMD by distilling state-of-the-art image and video generation models, including Qwen-Image (20B parameters) and Wan2.2 (28B parameters). Experimental results demonstrate that Phased DMD preserves output diversity better than DMD while retaining key generative capabilities. We will release our code and models.

sensenova SenseNova
·
Oct 31 1

SlimPajama-DC: Understanding Data Combinations for LLM Training

This paper aims to understand the impacts of various data combinations (e.g., web text, wikipedia, github, books) on the training of large language models using SlimPajama. SlimPajama is a rigorously deduplicated, multi-source dataset, which has been refined and further deduplicated to 627B tokens from the extensive 1.2T tokens RedPajama dataset contributed by Together. We've termed our research as SlimPajama-DC, an empirical analysis designed to uncover fundamental characteristics and best practices associated with employing SlimPajama in the training of large language models. During our research with SlimPajama, two pivotal observations emerged: (1) Global deduplication vs. local deduplication. We analyze and discuss how global (across different sources of datasets) and local (within the single source of dataset) deduplications affect the performance of trained models. (2) Proportions of high-quality/highly-deduplicated multi-source datasets in the combination. To study this, we construct six configurations of SlimPajama dataset and train individual ones using 1.3B Cerebras-GPT model with Alibi and SwiGLU. Our best configuration outperforms the 1.3B model trained on RedPajama using the same number of training tokens by a significant margin. All our 1.3B models are trained on Cerebras 16times CS-2 cluster with a total of 80 PFLOP/s in bf16 mixed precision. We further extend our discoveries (such as increasing data diversity is crucial after global deduplication) on a 7B model with large batch-size training. Our models and the separate SlimPajama-DC datasets are available at: https://huggingface.co/MBZUAI-LLM and https://huggingface.co/datasets/cerebras/SlimPajama-627B.

  • 8 authors
·
Sep 19, 2023 1

How Well Do LLMs Generate Code for Different Application Domains? Benchmark and Evaluation

Recently, an increasing number of AI-driven programming assistants powered by code LLMs have been integrated into various real-world software development environments, significantly boosting developer productivity. However, existing code generation benchmarks primarily focus on general-purpose scenarios, leaving the code generation performance of LLMs for specific application domains largely unknown. In this paper, we introduce a new benchmark, MultiCodeBench, to fill this gap. MultiCodeBench comprises 2,400 programming tasks, covering 12 popular software development domains and 15 programming languages. Specifically, we perform in-depth research to identify these 12 application domains. Given that each domain may involve multiple technical frameworks, and that different frameworks present distinct challenges in the coding process, we categorize the commonly used frameworks and platforms within each domain. We then sample programming problems from GitHub repositories related to these subdomains. To ensure the quality of the tasks and mitigate data leakage issues, we invite annotators to rewrite the docstrings for each task in MultiCodeBench. Additionally, we build a static analysis-based dependency parsing tool to extract the dependencies in the ground truth for each task, enabling deeper performance analysis. Through extensive experiments on MultiCodeBench with eleven representative mainstream LLMs, we reveal the code generation performance of the LLMs across different application domains, providing practical insights for developers in downstream fields when selecting LLMs. Furthermore, we analyze the reasons behind the models' failures in completing software application development tasks, offering guidance for model developers to enhance domain-specific code generation capabilities.

  • 5 authors
·
Dec 24, 2024

On the Efficacy of Differentially Private Few-shot Image Classification

There has been significant recent progress in training differentially private (DP) models which achieve accuracy that approaches the best non-private models. These DP models are typically pretrained on large public datasets and then fine-tuned on private downstream datasets that are relatively large and similar in distribution to the pretraining data. However, in many applications including personalization and federated learning, it is crucial to perform well (i) in the few-shot setting, as obtaining large amounts of labeled data may be problematic; and (ii) on datasets from a wide variety of domains for use in various specialist settings. To understand under which conditions few-shot DP can be effective, we perform an exhaustive set of experiments that reveals how the accuracy and vulnerability to attack of few-shot DP image classification models are affected as the number of shots per class, privacy level, model architecture, downstream dataset, and subset of learnable parameters in the model vary. We show that to achieve DP accuracy on par with non-private models, the shots per class must be increased as the privacy level increases. We also show that learning parameter-efficient FiLM adapters under DP is competitive with learning just the final classifier layer or learning all of the network parameters. Finally, we evaluate DP federated learning systems and establish state-of-the-art performance on the challenging FLAIR benchmark.

  • 8 authors
·
Feb 2, 2023

MultiRef: Controllable Image Generation with Multiple Visual References

Visual designers naturally draw inspiration from multiple visual references, combining diverse elements and aesthetic principles to create artwork. However, current image generative frameworks predominantly rely on single-source inputs -- either text prompts or individual reference images. In this paper, we focus on the task of controllable image generation using multiple visual references. We introduce MultiRef-bench, a rigorous evaluation framework comprising 990 synthetic and 1,000 real-world samples that require incorporating visual content from multiple reference images. The synthetic samples are synthetically generated through our data engine RefBlend, with 10 reference types and 33 reference combinations. Based on RefBlend, we further construct a dataset MultiRef containing 38k high-quality images to facilitate further research. Our experiments across three interleaved image-text models (i.e., OmniGen, ACE, and Show-o) and six agentic frameworks (e.g., ChatDiT and LLM + SD) reveal that even state-of-the-art systems struggle with multi-reference conditioning, with the best model OmniGen achieving only 66.6% in synthetic samples and 79.0% in real-world cases on average compared to the golden answer. These findings provide valuable directions for developing more flexible and human-like creative tools that can effectively integrate multiple sources of visual inspiration. The dataset is publicly available at: https://multiref.github.io/.

MixtureVitae: Open Web-Scale Pretraining Dataset With High Quality Instruction and Reasoning Data Built from Permissive-First Text Sources

We present MixtureVitae, an open-access pretraining corpus built to minimize legal risk while providing strong model performance. MixtureVitae follows a risk-mitigated sourcing strategy that combines public-domain and permissively licensed text (e.g., CC-BY/Apache) with carefully justified low-risk additions (e.g., government works and EU TDM-eligible sources), alongside targeted instruction, reasoning and synthetic data with documented provenance. We detail a transparent, multi-stage pipeline for license-aware filtering, safety and quality screening, and domain-aware mixing, and we release the dataset and curation recipes to support reproducible research. In controlled experiments using the open-sci-ref training protocol (fixed architectures at 130M/400M/1.3B/1.7B parameters; training budgets of 50B and 300B tokens), models trained on MixtureVitae consistently outperform other permissive datasets across a suite of standard benchmarks, and at the 1.7B/300B setting they surpass FineWeb-Edu and approach DCLM in the later stages of training. Performance is particularly strong on math/code and competitive on QA tasks. These results demonstrate that permissive-first, risk-mitigated data provides a practical and legally mitigated foundation for training capable LLMs, reducing reliance on indiscriminate web scraping without sacrificing competitiveness. Code: https://github.com/ontocord/mixturevitae

ontocord Ontocord.AI
·
Sep 29 3

Differentially Private Synthetic Data via Foundation Model APIs 2: Text

Text data has become extremely valuable due to the emergence of machine learning algorithms that learn from it. A lot of high-quality text data generated in the real world is private and therefore cannot be shared or used freely due to privacy concerns. Generating synthetic replicas of private text data with a formal privacy guarantee, i.e., differential privacy (DP), offers a promising and scalable solution. However, existing methods necessitate DP finetuning of large language models (LLMs) on private data to generate DP synthetic data. This approach is not viable for proprietary LLMs (e.g., GPT-3.5) and also demands considerable computational resources for open-source LLMs. Lin et al. (2024) recently introduced the Private Evolution (PE) algorithm to generate DP synthetic images with only API access to diffusion models. In this work, we propose an augmented PE algorithm, named Aug-PE, that applies to the complex setting of text. We use API access to an LLM and generate DP synthetic text without any model training. We conduct comprehensive experiments on three benchmark datasets. Our results demonstrate that Aug-PE produces DP synthetic text that yields competitive utility with the SOTA DP finetuning baselines. This underscores the feasibility of relying solely on API access of LLMs to produce high-quality DP synthetic texts, thereby facilitating more accessible routes to privacy-preserving LLM applications. Our code and data are available at https://github.com/AI-secure/aug-pe.

  • 12 authors
·
Mar 4, 2024

A Decentralized Retrieval Augmented Generation System with Source Reliabilities Secured on Blockchain

Existing retrieval-augmented generation (RAG) systems typically use a centralized architecture, causing a high cost of data collection, integration, and management, as well as privacy concerns. There is a great need for a decentralized RAG system that enables foundation models to utilize information directly from data owners who maintain full control over their sources. However, decentralization brings a challenge: the numerous independent data sources vary significantly in reliability, which can diminish retrieval accuracy and response quality. To address this, our decentralized RAG system has a novel reliability scoring mechanism that dynamically evaluates each source based on the quality of responses it contributes to generate and prioritizes high-quality sources during retrieval. To ensure transparency and trust, the scoring process is securely managed through blockchain-based smart contracts, creating verifiable and tamper-proof reliability records without relying on a central authority. We evaluate our decentralized system with two Llama models (3B and 8B) in two simulated environments where six data sources have different levels of reliability. Our system achieves a +10.7\% performance improvement over its centralized counterpart in the real world-like unreliable data environments. Notably, it approaches the upper-bound performance of centralized systems under ideally reliable data environments. The decentralized infrastructure enables secure and trustworthy scoring management, achieving approximately 56\% marginal cost savings through batched update operations. Our code and system are open-sourced at github.com/yining610/Reliable-dRAG.

  • 5 authors
·
Nov 10 2

DARE the Extreme: Revisiting Delta-Parameter Pruning For Fine-Tuned Models

Storing open-source fine-tuned models separately introduces redundancy and increases response times in applications utilizing multiple models. Delta-parameter pruning (DPP), particularly the random drop and rescale (DARE) method proposed by Yu et al., addresses this by pruning the majority of delta parameters--the differences between fine-tuned and pre-trained model weights--while typically maintaining minimal performance loss. However, DARE fails when either the pruning rate or the magnitude of the delta parameters is large. We highlight two key reasons for this failure: (1) an excessively large rescaling factor as pruning rates increase, and (2) high mean and variance in the delta parameters. To push DARE's limits, we introduce DAREx (DARE the eXtreme), which features two algorithmic improvements: (1) DAREx-q, a rescaling factor modification that significantly boosts performance at high pruning rates (e.g., >30 % on COLA and SST2 for encoder models, with even greater gains in decoder models), and (2) DAREx-L2, which combines DARE with AdamR, an in-training method that applies appropriate delta regularization before DPP. We also demonstrate that DAREx-q can be seamlessly combined with vanilla parameter-efficient fine-tuning techniques like LoRA and can facilitate structural DPP. Additionally, we revisit the application of importance-based pruning techniques within DPP, demonstrating that they outperform random-based methods when delta parameters are large. Through this comprehensive study, we develop a pipeline for selecting the most appropriate DPP method under various practical scenarios.

  • 6 authors
·
Oct 11, 2024

EasyTPP: Towards Open Benchmarking Temporal Point Processes

Continuous-time event sequences play a vital role in real-world domains such as healthcare, finance, online shopping, social networks, and so on. To model such data, temporal point processes (TPPs) have emerged as the most natural and competitive models, making a significant impact in both academic and application communities. Despite the emergence of many powerful models in recent years, there hasn't been a central benchmark for these models and future research endeavors. This lack of standardization impedes researchers and practitioners from comparing methods and reproducing results, potentially slowing down progress in this field. In this paper, we present EasyTPP, the first central repository of research assets (e.g., data, models, evaluation programs, documentations) in the area of event sequence modeling. Our EasyTPP makes several unique contributions to this area: a unified interface of using existing datasets and adding new datasets; a wide range of evaluation programs that are easy to use and extend as well as facilitate reproducible research; implementations of popular neural TPPs, together with a rich library of modules by composing which one could quickly build complex models. All the data and implementation can be found at https://github.com/ant-research/EasyTemporalPointProcess. We will actively maintain this benchmark and welcome contributions from other researchers and practitioners. Our benchmark will help promote reproducible research in this field, thus accelerating research progress as well as making more significant real-world impacts.

  • 12 authors
·
Jul 16, 2023

Improving Single-Image Defocus Deblurring: How Dual-Pixel Images Help Through Multi-Task Learning

Many camera sensors use a dual-pixel (DP) design that operates as a rudimentary light field providing two sub-aperture views of a scene in a single capture. The DP sensor was developed to improve how cameras perform autofocus. Since the DP sensor's introduction, researchers have found additional uses for the DP data, such as depth estimation, reflection removal, and defocus deblurring. We are interested in the latter task of defocus deblurring. In particular, we propose a single-image deblurring network that incorporates the two sub-aperture views into a multi-task framework. Specifically, we show that jointly learning to predict the two DP views from a single blurry input image improves the network's ability to learn to deblur the image. Our experiments show this multi-task strategy achieves +1dB PSNR improvement over state-of-the-art defocus deblurring methods. In addition, our multi-task framework allows accurate DP-view synthesis (e.g., ~39dB PSNR) from the single input image. These high-quality DP views can be used for other DP-based applications, such as reflection removal. As part of this effort, we have captured a new dataset of 7,059 high-quality images to support our training for the DP-view synthesis task. Our dataset, code, and trained models are publicly available at https://github.com/Abdullah-Abuolaim/multi-task-defocus-deblurring-dual-pixel-nimat.

  • 3 authors
·
Aug 11, 2021

Dataset Distillation via Committee Voting

Dataset distillation aims to synthesize a smaller, representative dataset that preserves the essential properties of the original data, enabling efficient model training with reduced computational resources. Prior work has primarily focused on improving the alignment or matching process between original and synthetic data, or on enhancing the efficiency of distilling large datasets. In this work, we introduce {bf C}ommittee {bf V}oting for {bf D}ataset {bf D}istillation (CV-DD), a novel and orthogonal approach that leverages the collective wisdom of multiple models or experts to create high-quality distilled datasets. We start by showing how to establish a strong baseline that already achieves state-of-the-art accuracy through leveraging recent advancements and thoughtful adjustments in model design and optimization processes. By integrating distributions and predictions from a committee of models while generating high-quality soft labels, our method captures a wider spectrum of data features, reduces model-specific biases and the adverse effects of distribution shifts, leading to significant improvements in generalization. This voting-based strategy not only promotes diversity and robustness within the distilled dataset but also significantly reduces overfitting, resulting in improved performance on post-eval tasks. Extensive experiments across various datasets and IPCs (images per class) demonstrate that Committee Voting leads to more reliable and adaptable distilled data compared to single/multi-model distillation methods, demonstrating its potential for efficient and accurate dataset distillation. Code is available at: https://github.com/Jiacheng8/CV-DD.

  • 6 authors
·
Jan 13