论文检索

Miscellaneous Aspects of Machine Learning · Unsupervised and Semi-supervised Learning

Shengju Yu, Zhibin Dong, Siwei Wang, Pei Zhang, Yi Zhang, Xinwang Liu, Thomas Guan, Tiejun Li, Yiu-ming Cheung

Most of incomplete multi-view clustering (IMVC) methods typically choose to ignore the missing samples and only utilize observed unpaired samples to construct bipartite similarity. Moreover, they employ a single quantity of prototypes to extract the information of $\textbf{all}$ views. To eliminate these drawbacks, we present a simple yet effective IMVC approach, SIIHPC, in this work. It firstly transforms partial bipartition learning into original sample form by virtue of reconstruction concept to split out of observed similarity, and then loosens traditional non-negative constraints via regularizing samples to more freely characterize the similarity. Subsequently, it learns to recover the incomplete parts by utilizing the connection built between the similarity exclusive on respective view and the consensus graph shared for all views. On this foundation, it further introduces a group of hybrid prototype quantities for each individual view to flexibly extract the data features belonging to each view itself. Accordingly, the resulting graphs are with various scales and describe the overall similarity more comprehensively. It is worth mentioning that these all are optimized in one unified learning framework, which makes it possible for them to reciprocally promote. Then, to effectively solve the formulated optimization problem, we design an ingenious auxiliary function that is with theoretically proven monotonic-increasing properties. Finally, the clustering results are obtained by implementing spectral grouping action on the eigenvectors of stacked multi-scale consensus similarity. Experimental results confirm the effectiveness of SIIHPC.

Miscellaneous Aspects of Machine Learning · Unsupervised and Semi-supervised Learning

Yi Zhang, Siwei Wang, Jiyuan Liu, Shengju Yu, Zhibin Dong, Suyuan Liu, Xinwang Liu, En Zhu

Recent advancements in multiple kernel clustering (MKC) have highlighted the effectiveness of late fusion strategies, particularly in enhancing computational efficiency to near-linear complexity while achieving promising clustering performance. However, existing methods encounter three significant limitations: (1) reliance on fixed base partition matrices that do not adaptively optimize during the clustering process, thereby constraining their performance to the inherent representational capabilities of these matrices; (2) a focus on adjusting kernel weights to explore inter-view consistency and complementarity, which often neglects the intrinsic high-order correlations among views, thereby limiting the extraction of comprehensive multiple kernel information; (3) a lack of adaptive mechanisms to accommodate varying distributions within the data, which limits robustness and generalization. To address these challenges, this paper proposes a novel algorithm termed Dynamic Late Fusion Multiple Kernel Clustering with Robust {Tensor Learning via min-max optimization (DLEFT-MKC), which effectively overcomes the representational bottleneck of base partition matrices and facilitates the learning of meaningful high-order cross-view information. Specifically, it is the first to incorporate a min-max optimization paradigm into tensor-based MKC, enhancing algorithm robustness and generalization. Additionally, it dynamically reconstructs decision layers to enhance representation capabilities and subsequently stacks the reconstructed representations for tensor learning that promotes the capture of high-order associations and cluster structures across views, ultimately yielding consensus clustering partitions. To solve the resultant optimization problem, we innovatively design a strategy that combines reduced gradient descent with the alternating direction method of multipliers, ensuring convergence to local optima while maintaining high computational efficiency. Extensive experimental results across various benchmark datasets validate the superior effectiveness and efficiency of the proposed DLEFT-MKC.

Yi-Kai Zhang, Shiyin Lu, Qing-Guo Chen, De-Chuan Zhan, Han-Jia Ye

Multimodal Large Language Models (MLLMs) are thriving through continuous fine-tuning by LLMs. Driven by the law that "scale is everything", MLLMs expand their training sets during version iterations. In this paper, we propose a large-scale training data engine built around an evaluating-exploring-evolving (E3) loop. Evaluating the data provides insights into its characteristics. Exploring quality rules helps identify which data enhances training. Together, these processes facilitate the systematic evolution of new, high-quality data. With the E3 loop, we introduce ZooProbe, an efficient data engine for MLLMs. First, the problem of data expansion is formalized as a tree of sampling and growth. ZooProbe introduces a small-scale model *zoo* to obtain comprehensive evaluations for child datasets. From multiple perspectives, visual, textual, and multimodal models cover over 50 dimensions of intrinsic and meta attributes, such as object and topic distribution, and higher-level properties, like annotation quality and scene complexity. ZooProbe constructs based on A$^\star$ search, modeling the heuristic function as a quality estimate from data evaluation results. It dynamically explores the rule of data quality based on the model state of the *probe* datasets. Additionally, it evolves new targeted data with identified high-quality rules. We also develop an extra heuristic quality ranker with the data utilized and discarded during the expansion. Our experiments show that ZooProbe significantly breaks the scaling law in multimodal instruction fine-tuning at scales of 260$k$ and below.ZooProbe generates high-quality data that accelerates MLLM training and enhances performance, automating the evolution of large-scale training data.

Deep Learning · Other Representation Learning

Paul Gavrikov, Jovita Lukasik, Steffen Jung, Robert Geirhos, Muhammad Jehanzeb Mirza, Margret Keuper, Janis Keuper

Unlike traditional vision-only models, vision language models (VLMs) offer an intuitive way to access visual content through language prompting by combining a large language model (LLM) with a vision encoder. However, both the LLM and the vision encoder come with their own set of biases, cue preferences, and shortcuts, which have been rigorously studied in uni-modal models. A timely question is how such (potentially misaligned) biases and cue preferences behave under multi-modal fusion in VLMs. As a first step towards a better understanding, we investigate a particularly well-studied vision-only bias - the texture vs. shape bias and the dominance of local over global information. As expected, we find that VLMs inherit this bias to some extent from their vision encoders. Surprisingly, the multi-modality alone proves to have important effects on the model behavior, i.e., the joint training and the language querying change the way visual cues are processed. While this direct impact of language-informed training on a model's visual perception is intriguing, it raises further questions on our ability to actively steer a model's output so that its prediction is based on particular visual cues of the user's choice. Interestingly, VLMs have an inherent tendency to recognize objects based on shape information, which is different from what a plain vision encoder would do. Further active steering towards shape-based classifications through language prompts is however limited. In contrast, active VLM steering towards texture-based decisions through simple natural language prompts is often more successful.

Xinmeng Xu, Yiqun Zhang, Jizhen Li, Yuhong Yang, Yong Luo, Weiping Tu

Current deep neural networks for speech enhancement (SE) aim to minimize the distance between the output signal and the clean target by filtering out noise features from input features. However, when noise and speech components are highly similar, SE models struggle to learn effective discrimination patterns. To address this challenge, we propose a Filter-Recycle-Interguide framework termed Filter-Recycle-INterGuide NETwork (FIRING-Net) for SE, which filters the input features to extract target features and recycles the filtered-out features as non-target features. These two feature sets then guide each other to refine the features, leading to the aggregation of speech information within the target features and noise information within the non-target features. The proposed FIRING-Net mainly consists of a Local Module (LM) and a Global Module (GM). The LM uses outputs of the speech extraction network as target features and the residual between input and output as non-target features. The GM leverages the energy distribution of self-attention map to extract target and non-target features guided by highest and lowest energy regions. Both LM and GM include interaction modules to leverage the two feature sets in an inter-guided manner for collecting speech from non-target features and filtering out noise from target features. Experiments confirm the effectiveness of the Filter-Recycle-Interguide framework, with FIRING-Net achieving a strong balance between SE performance and computational efficiency, surpassing comparable models across various SNR levels and noise environments.

Li Huaqiu, HuXiaowan, Haoqian Wang

Real-world low-light images often suffer from complex degradations such as local overexposure, low brightness, noise, and uneven illumination. Supervised methods tend to overfit to specific scenarios, while unsupervised methods, though better at generalization, struggle to model these degradations due to the lack of reference images. To address this issue, we propose an interpretable, zero-reference joint denoising and low-light enhancement framework tailored for real-world scenarios. Our method derives a training strategy based on paired sub-images with varying illumination and noise levels, grounded in physical imaging principles and retinex theory. Additionally, we leverage the Discrete Cosine Transform (DCT) to perform frequency domain decomposition in the sRGB space, and introduce an implicit-guided hybrid representation strategy that effectively separates intricate compounded degradations. In the backbone network design, we develop retinal decomposition network guided by implicit degradation representation mechanisms. Extensive experiments demonstrate the superiority of our method. Code will be available at https://github.com/huaqlili/unsupervised-light-enhance-ICLR2025.

Social Aspects · Accountability, Transparency and Interpretability

Chaoyi Zhu, Jiayi Tang, Jeroen Galjaard, Pin-Yu Chen, Robert Birke, Cornelis Bos, Lydia Chen

Synthetic data offers alternatives for data augmentation and sharing. Till date, it remains unknown how to use watermarking techniques to trace and audit synthetic tables generated by tabular diffusion models to mitigate potential misuses. In this paper, we design TabWak, the first watermarking method to embed invisible signatures that control the sampling of Gaussian latent codes used to synthesize table rows via the diffusion backbone. TabWak has two key features. Different from existing image watermarking techniques, TabWak uses self-cloning and shuffling to embed the secret key in positional information of random seeds that control the Gaussian latents, allowing to use different seeds at each row for high inter-row diversity and enabling row-wise detectability. To further boost the robustness of watermark detection against post-editing attacks, TabWak uses a valid-bit mechanism that focuses on the tail of the latent code distribution for superior noise resilience. We provide theoretical guarantees on the row diversity and effectiveness of detectability. We evaluate TabWak on five datasets against baselines to show that the quality of watermarked tables remains nearly indistinguishable from non-watermarked tables while achieving high detectability in the presence of strong post-editing attacks, with a 100% true positive rate at a 0.1% false positive rate on synthetic tables with fewer than 300 rows. Our code is available at the following anonymized repository https://github.com/chaoyitud/TabWak.

Deep Learning · Large Language Models

Ke Yang, Yao Liu, Sapana Chaudhary, Rasool Fakoor, Pratik A Chaudhari, George Karypis, Huzefa Rangwala

Autonomy via agents based on large language models (LLMs) that can carry out personalized yet standardized tasks presents a significant opportunity to drive human efficiency. There is an emerging need and interest in automating web tasks (e.g., booking a hotel for a given date within a budget). Being a practical use case itself, the web agent also serves as an important proof-of-concept example for various agent grounding scenarios, with its success promising advancements in many future applications. Meanwhile, much prior research focuses on handcrafting their web agent strategies (e.g., agent's prompting templates, reflective workflow, role-play and multi-agent systems, search or sampling methods, etc.) and the corresponding in-context examples. However, these custom strategies often struggle with generalizability across all potential real-world applications. On the other hand, there has been limited study on the misalignment between a web agent's observation and action representation, and the data on which the agent's underlying LLM has been pre-trained. This discrepancy is especially notable when LLMs are primarily trained for language completion rather than tasks involving embodied navigation actions and symbolic web elements. In our study, we enhance an LLM-based web agent by simply refining its observation and action space, aligning these more closely with the LLM's capabilities. This approach enables our base agent to significantly outperform previous methods on a wide variety of web tasks. Specifically, on WebArena, a benchmark featuring general-purpose web interaction tasks, our agent AgentOccam surpasses the previous state-of-the-art and concurrent work by 9.8 (+29.4%) and 5.9 (+15.8%) absolute points respectively, and boosts the success rate by 26.6 points (+161%) over similar plain web agents with its observation and action space alignment. Furthermore, on WebVoyager benchmark comprising tasks defined on real-world websites, AgentOccam exceeds the former best agent by 2.4 points (+4.6%) on tasks with deterministic answers. We achieve this without using in-context examples, new agent roles, online feedback or search strategies. AgentOccam's simple design highlights LLMs' impressive zero-shot performance on web tasks, and underlines the critical role of carefully tuning observation and action spaces for LLM-based agents.

Peng Dai, Feitong Tan, Qiangeng Xu, David Futschik, Ruofei Du, Sean Fanello, XIAOJUAN QI, Yinda Zhang

Video generation models have demonstrated great capability of producing impressive monocular videos, however, the generation of 3D stereoscopic video remains under-explored. We propose a pose-free and training-free approach for generating 3D stereoscopic videos using an off-the-shelf monocular video generation model. Our method warps a generated monocular video into camera views on stereoscopic baseline using estimated video depth, and employs a novel frame matrix video inpainting framework. The framework leverages the video generation model to inpaint frames observed from different timestamps and views. This effective approach generates consistent and semantically coherent stereoscopic videos without scene optimization or model fine-tuning. Moreover, we develop a disocclusion boundary re-injection scheme that further improves the quality of video inpainting by alleviating the negative effects propagated from disoccluded areas in the latent space. We validate the efficacy of our proposed method by conducting experiments on videos from various generative models, including Sora [4], Lumiere [2], WALT [8], and Zeroscope [12]. The experiments demonstrate that our method has a significant improvement over previous methods. Project page at https://daipengwa.github.io/SVG_ProjectPage/

Miscellaneous Aspects of Machine Learning · Unsupervised and Semi-supervised Learning

Zhaolong Du, Shasha Mao, Xuequan Lu, Mengnan Qi, Yimeng Zhang, Jing Gu, Licheng Jiao

Multiple-instance learning (MIL) was initially proposed to identify key instances within a set (bag) of instances when only one bag-level label is provided. Current deep MIL models mostly solve multi-instance problem in feature space. Nevertheless, with the increasing complexity of data, we found this paradigm faces significant risks in representation learning stage, which could lead to algorithm degradation in deep MIL models. We speculate that the degradation issue stems from the persistent drift of instances in feature space during learning. In this paper, we propose a novel Probability-Space MIL network (PSMIL) as a countermeasure. In PSMIL, a self-training alignment strategy is introduced in probability space to cope with the drift problem in feature space, and the alignment target objective is proven mathematically optimal. Furthermore, we reveal that the widely-used attention-based pooling mechanism in current deep MIL models is easily affected by the perturbation in feature space and further introduce an alternative called probability-space attention pooling. It effectively captures the key instance in each bag from feature space to probability space, and further eliminates the impact of selection drift in the pooling stage. To summarize, PSMIL seeks to solve a MIL problem in probability space rather than feature space. Experimental results illustrate that PSMIL could potentially achieve performance close to supervised learning level in complex tasks (gap within 5\%), with the incremental alignment in propability space bring more than 19\% accuracy improvements for current existing mainstream models in simulated CIFAR datasets. For existing publicly available MIL benchmarks/datasets, attention in probability space also achieves competitive performance to the state-of-the-art deep MIL models. Codes are available at \url{https://github.com/LMBDA-design/PSAMIL}.

Applications · Physics

Sifan Wang, Jacob Seidman, Shyam Sankaran, Hanwen Wang, George Pappas, Paris Perdikaris

Operator learning, which aims to approximate maps between infinite-dimensional function spaces, is an important area in scientific machine learning with applications across various physical domains. Here we introduce the Continuous Vision Transformer (CViT), a novel neural operator architecture that leverages advances in computer vision to address challenges in learning complex physical systems. CViT combines a vision transformer encoder, a novel grid-based coordinate embedding, and a query-wise cross-attention mechanism to effectively capture multi-scale dependencies. This design allows for flexible output representations and consistent evaluation at arbitrary resolutions. We demonstrate CViT's effectiveness across a diverse range of partial differential equation (PDE) systems, including fluid dynamics, climate modeling, and reaction-diffusion processes. Our comprehensive experiments show that CViT achieves state-of-the-art performance on multiple benchmarks, often surpassing larger foundation models, even without extensive pretraining and roll-out fine-tuning. Taken together, CViT exhibits robust handling of discontinuous solutions, multi-scale features, and intricate spatio-temporal dynamics. Our contributions can be viewed as a significant step towards adapting advanced computer vision architectures for building more flexible and accurate machine learning models in the physical sciences.

Applications · Computer Vision

Leqi Shen, Tianxiang Hao, Tao He, Sicheng Zhao, Yifeng Zhang, pengzhang liu, Yongjun Bao, Guiguang Ding

Most text-video retrieval methods utilize the text-image pre-trained models like CLIP as a backbone. These methods process each sampled frame independently by the image encoder, resulting in high computational overhead and limiting practical deployment. Addressing this, we focus on efficient text-video retrieval by tackling two key challenges: 1. From the perspective of trainable parameters, current parameter-efficient fine-tuning methods incur high inference costs; 2. From the perspective of model complexity, current token compression methods are mainly designed for images to reduce spatial redundancy but overlook temporal redundancy in consecutive frames of a video. To tackle these challenges, we propose Temporal Token Merging (TempMe), a parameter-efficient and training-inference efficient text-video retrieval architecture that minimizes trainable parameters and model complexity. Specifically, we introduce a progressive multi-granularity framework. By gradually combining neighboring clips, we reduce spatio-temporal redundancy and enhance temporal modeling across different frames, leading to improved efficiency and performance. Extensive experiments validate the superiority of our TempMe. Compared to previous parameter-efficient text-video retrieval methods, TempMe achieves superior performance with just 0.50M trainable parameters. It significantly reduces output tokens by 95% and GFLOPs by 51%, while achieving a 1.8X speedup and a 4.4% R-Sum improvement. With full fine-tuning, TempMe achieves a significant 7.9% R-Sum improvement, trains 1.57X faster, and utilizes 75.2% GPU memory usage. The code is available at https://github.com/LunarShen/TempMe.

Reinforcement Learning · Batch/Offline

Ahana Deb, Roberto Cipollone, Anders Jonsson, Alessandro Ronca, Mohammad Sadegh Talebi

This work studies offline Reinforcement Learning (RL) in a class of non-Markovian environments called Regular Decision Processes (RDPs). In RDPs, the unknown dependency of future observations and rewards from the past interactions can be captured by some hidden finite-state automaton. For this reason, many RDP algorithms first reconstruct this unknown dependency using automata learning techniques. In this paper, we consider episodic RDPs and show that it is possible to overcome the limitations of existing offline RL algorithms for RDPs viathe introduction of two original techniques: a novel metric grounded in formal language theory and an approach based on Count-Min-Sketch (CMS). Owing to the novel language metric, our algorithm is proven to be more sample efficient than existing results, and in some problem instances admitting low complexity languages, the gain is showcased to be exponential in the episode length. The CMS-based approach removes the need for naïve counting and alleviates the memory requirements for long planning horizons. We derive Probably Approximately Correct (PAC) sample complexity bounds associated to each of these techniques, and validate the approach experimentally.

Deep Learning · Algorithms

Rui Hu, Yifan Zhang, Zhuoran Li, Longbo Huang

Generative Flow Networks (GFlowNets) are a novel class of generative models designed to sample from unnormalized distributions and have found applications in various important tasks, attracting great research interest in their training algorithms. In general, GFlowNets are trained by fitting the forward flow to the backward flow on sampled training objects. Prior work focused on the choice of training objects, parameterizations, sampling and resampling strategies, and backward policies, aiming to enhance credit assignment, exploration, or exploitation of the training process. However, the choice of regression loss, which can highly influence the exploration and exploitation behavior of the under-training policy, has been overlooked. Due to the lack of theoretical understanding for choosing an appropriate regression loss, most existing algorithms train the flow network by minimizing the squared error of the forward and backward flows in log-space, i.e., using the quadratic regression loss. In this work, we rigorously prove that distinct regression losses correspond to specific divergence measures, enabling us to design and analyze regression losses according to the desired properties of the corresponding divergence measures. Specifically, we examine two key properties: zero-forcing and zero-avoiding, where the former promotes exploitation and higher rewards, and the latter encourages exploration and enhances diversity. Based on our theoretical framework, we propose three novel regression losses, namely, Shifted-Cosh, Linex(1/2), and Linex(1). We evaluate them across three benchmarks: hyper-grid, bit-sequence generation, and molecule generation. Our proposed losses are compatible with most existing training algorithms, and significantly improve the performances of the algorithms concerning convergence speed, sample diversity, and robustness.

Reinforcement Learning · Batch/Offline

Gwangpyo Yoo, Honguk Woo

Offline reinforcement learning (RL) is becoming critical in risk-sensitive areas such as finance and autonomous driving, where incorrect decisions can lead to substantial financial loss or compromised safety. However, traditional risk-sensitive offline RL methods often struggle with accurately assessing risk, with minor errors in the estimated return potentially causing significant inaccuracies of risk estimation. These challenges are intensified by distribution shifts inherent in offline RL. To mitigate these issues, we propose a model risk-sensitive offline RL framework designed to minimize the worst-case of risks across a set of plausible alternative scenarios rather than solely focusing on minimizing estimated risk. We present a critic-ensemble criterion method that identifies the plausible alternative scenarios without introducing additional hyperparameters. We also incorporate the learned Fourier feature framework and the IQN framework to address spectral bias in neural networks, which can otherwise lead to severe errors in calculating model risk. Our experiments in finance and self-driving scenarios demonstrate that the proposed framework significantly reduces risk, by $11.2\%$ to $18.5\%$, compared to the most outperforming risk-sensitive offline RL baseline, particularly in highly uncertain environments.

Deep Learning · Generative Models and Autoencoders

Xierui Wang, Siming Fu, Qihan Huang, Wanggui He, Hao Jiang

Recent advancements in text-to-image generation models have dramatically enhanced the generation of photorealistic images from textual prompts, leading to an increased interest in personalized text-to-image applications, particularly in multi-subject scenarios. However, these advances are hindered by two main challenges: firstly, the need to accurately maintain the details of each referenced subject in accordance with the textual descriptions; and secondly, the difficulty in achieving a cohesive representation of multiple subjects in a single image without introducing inconsistencies. To address these concerns, our research introduces the MS-Diffusion framework for layout-guided zero-shot image personalization with multi-subjects. This innovative approach integrates grounding tokens with the feature resampler to maintain detail fidelity among subjects. With the layout guidance, MS-Diffusion further improves the cross-attention to adapt to the multi-subject inputs, ensuring that each subject condition acts on specific areas. The proposed multi-subject cross-attention orchestrates harmonious inter-subject compositions while preserving the control of texts. Comprehensive quantitative and qualitative experiments affirm that this method surpasses existing models in both image and text fidelity, promoting the development of personalized text-to-image generation.

Miscellaneous Aspects of Machine Learning · Unsupervised and Semi-supervised Learning

Yalong Jiang

Video anomaly detection (VAD) aims to identify novel actions or events which are unseen during training. Existing mainstream VAD techniques typically focus on the global patterns with redundant details and struggle to generalize to unseen samples. In this paper, we propose a framework that identifies the local patterns which generalize to novel samples and models the dynamics of local patterns. The capability of extracting spatial local patterns is achieved through a two-stage process involving image-text alignment and cross-modality attention. Generalizable representations are built by focusing on semantically relevant components which can be recombined to capture the essence of novel anomalies, reducing unnecessary visual data variances. To enhance local patterns with temporal clues, we propose a State Machine Module (SMM) that utilizes earlier high-resolution textual tokens to guide the generation of precise captions for subsequent low-resolution observations. Furthermore, temporal motion estimation complements spatial local patterns to detect anomalies characterized by novel spatial distributions or distinctive dynamics. Extensive experiments on popular benchmark datasets demonstrate the achievement of state-of-the-art performance. Code is available at https://github.com/AllenYLJiang/Local-Patterns-Generalize-Better/.

Applications · Physics

Bocheng Zeng, Qi Wang, Mengtao Yan, Yang Liu, Ruizhi Chengze, Yi Zhang, Hongsheng Liu, Zidong Wang, Hao Sun

Solving partial differential equations (PDEs) serves as a cornerstone for modeling complex dynamical systems. Recent progresses have demonstrated grand benefits of data-driven neural-based models for predicting spatiotemporal dynamics (e.g., tremendous speedup gain compared with classical numerical methods). However, most existing neural models rely on rich training data, have limited extrapolation and generalization abilities, and suffer to produce precise or reliable physical prediction under intricate conditions (e.g., irregular mesh or geometry, complex boundary conditions, diverse PDE parameters, etc.). To this end, we propose a new graph learning approach, namely, Physics-encoded Message Passing Graph Network (PhyMPGN), to model spatiotemporal PDE systems on irregular meshes given small training datasets. Specifically, we incorporate a GNN into a numerical integrator to approximate the temporal marching of spatiotemporal dynamics for a given PDE system. Considering that many physical phenomena are governed by diffusion processes, we further design a learnable Laplace block, which encodes the discrete Laplace-Beltrami operator, to aid and guide the GNN learning in a physically feasible solution space. A boundary condition padding strategy is also designed to improve the model convergence and accuracy. Extensive experiments demonstrate that PhyMPGN is capable of accurately predicting various types of spatiotemporal dynamics on coarse unstructured meshes, consistently achieves the state-of-the-art results, and outperforms other baselines with considerable gains.

Applications · Genetics, Cell Biology, Health, etc

Menghua (Rachel) Wu, Russell Littman, Jacob Levine, Lin Qiu, Tommaso Biancalani, David Richmond, Jan-Christian Huetter

High-content perturbation experiments allow scientists to probe biomolecular systems at unprecedented resolution, but experimental and analysis costs pose significant barriers to widespread adoption. Machine learning has the potential to guide efficient exploration of the perturbation space and extract novel insights from these data. However, current approaches neglect the semantic richness of the relevant biology, and their objectives are misaligned with downstream biological analyses. In this paper, we hypothesize that large language models (LLMs) present a natural medium for representing complex biological relationships and rationalizing experimental outcomes. We propose PerturbQA, a benchmark for structured reasoning over perturbation experiments. Unlike current benchmarks that primarily interrogate existing knowledge, PerturbQA is inspired by open problems in perturbation modeling: prediction of differential expression and change of direction for unseen perturbations, and gene set enrichment. We evaluate state-of-the-art machine learning and statistical approaches for modeling perturbations, as well as standard LLM reasoning strategies, and we find that current methods perform poorly on PerturbQA. As a proof of feasibility, we introduce Summer (SUMMarize, retrievE, and answeR, a simple, domain-informed LLM framework that matches or exceeds the current state-of-the-art. Our code and data are publicly available at https://github.com/genentech/PerturbQA.

Miscellaneous Aspects of Machine Learning · Supervised Learning

Lun Wang

Micro-batch clipping, a gradient clipping method, has recently shown potential in enhancing auto-speech recognition (ASR) model performance. However, the underlying mechanism behind this improvement remains mysterious, particularly the observation that only certain micro-batch sizes are beneficial. In this paper, we make the first attempt to explain this phenomenon. Inspired by recent data pruning research, we assume that specific training samples may impede model convergence during certain training phases. Under this assumption, the convergence analysis shows that micro-batch clipping can improve the convergence rate asymptotically at the cost of an additional constant bias that does not diminish with more training iterations. The bias is dependent on a few factors and can be minimized at specific micro-batch size, thereby elucidating the existence of the sweet-spot micro-batch size observed previously. We also verify the effectiveness of micro-batch clipping beyond speech models on vision and language models, and show promising performance gains in these domains. An exploration of potential limitations shows that micro-batch clipping is less effective when training data originates from multiple distinct domains.