论文检索

Applications

Yuhao Wang, Qiang Zhang, Ming Qin, Xiang Zhuang, Xiaotong Li, Zhichen Gong, Zeyuan Wang, Yu Zhao, Jianhua Yao, Keyan Ding 等

Directed evolution, a cornerstone of protein optimization, is to harness natural mutational processes to enhance protein functionality. Existing Machine Learning-assisted Directed Evolution (MLDE) methodologies typically rely on data-driven strategies and often overlook the profound domain knowledge in biochemical fields. In this paper, we introduce a novel Knowledge-aware Reinforced Language Model (KnowRLM) for MLDE. An Amino Acid Knowledge Graph (AAKG) is constructed to represent the intricate biochemical relationships among amino acids. We further propose a Protein Language Model (PLM)-based policy network that iteratively samples mutants through preferential random walks on the AAKG using a dynamic sliding window mechanism. The novel mutants are actively sampled to fine-tune a fitness predictor as the reward model, providing feedback to the knowledge-aware policy. Finally, we optimize the whole system in an active learning approach that mimics biological settings in practice.KnowRLM stands out for its ability to utilize contextual amino acid information from knowledge graphs, thus attaining advantages from both statistical patterns of protein sequences and biochemical properties of amino acids.Extensive experiments demonstrate the superior performance of KnowRLM in more efficiently identifying high-fitness mutants compared to existing methods.

Deep Learning

Haoyang Li, Xin Wang, Zeyang Zhang, Haibo Chen, Ziwei Zhang, Wenwu Zhu

Graph out-of-distribution (OOD) generalization, aiming to generalize graph neural networks (GNNs) under distribution shifts between training and testing environments, has attracted ever-increasing attention recently. However, existing literature heavily relies on sufficient task-dependent graph labels, which are often scarce or even unavailable, limiting their applications in real-world scenarios. In this paper, we study the self-supervised graph OOD generalization problem, i.e., learning GNNs capable of achieving relatively stable performances under distribution shifts without graph labels. However, the problem remains largely unexplored, with the critical challenge that the invariant and variant information are highly entangled in graphs. To solve this problem, we propose an OOD generalized disentangled graph contrastive learning model (OOD-GCL), which is capable of learning disentangled graph-level representations with self-supervision that can handle distribution shifts between training and testing graph data. Specifically, we first introduce a disentangled graph encoder to map each input graph into the factorized graph representation. Then we propose a tailored disentangled invariant self-supervised learning module to maximize predictive ability of the representations and make sure the representations other than from one specific channel are invariant to the environments partitioned by this latent factor for excluding the information corresponding to this latent factor for disentanglement. Finally, the disentangled graph representations are fed into a linear predictor and finetuned for the downstream tasks. We provide comprehensive theoretical analyses to show that our model can learn disentangled graph representations and achieve OOD generalization. Extensive experiments on real-world datasets demonstrate the superiority of our model against state-of-the-art baselines under distribution shifts for graph classification tasks.

Deep Learning · Graph Neural Networks

Zeyang Zhang, Xin Wang, Yijian Qin, Hong Chen, Ziwei Zhang, Xu Chu, Wenwu Zhu

The existing graph neural architecture search (GNAS) methods assume that the graph tasks are static during the search process, ignoring the ubiquitous scenarios where sequential graph tasks come in a continual fashion. Moreover, existing GNAS works resort to entangled graph factors during the architecture search process, resulting in the catastrophic forgetting problems. In this paper, we study the problem of continual graph neural architecture search that is expected to continually search the architecture to learn new graph tasks without forgetting the past, which remains largely unexplored in the literature. However, this problem poses the challenge of architecture conflicts, i.e., the optimal architecture for the new graph task may have performance deterioration and thus sub-optimal for past tasks. To address the challenge, we propose a novel Disentangled Continual Graph Neural Architecture Search with Invariant Modularization (GASIM) method, which is able to continually search the optimal architectures without forgetting past knowledge. Specifically, we first design a modular graph architecture super-network incorporating multiple modules to enable searching architecture with factor expertise. Second, we propose a factor-based task-module router that discovers the latent graph factors and routes the incoming task to the best suitable architecture module to alleviate the forgetting problem induced by architecture conflicts. Finally, we propose an invariant architecture search mechanism to capture the shared knowledge among tasks. Extensive experiments on real-world datasets demonstrate that the proposed method achieves state-of-the-art performance against baselines in continual graph neural architecture search.

Applications · Language, Speech and Dialog

Weike Fang, Zhejian Zhou, Junzhou He, Weihang Wang

WebAssembly enables near-native execution in web applications and is increasingly adopted for tasks that demand high performance and robust security. However, its assembly-like syntax, implicit stack machine, and low-level data types make it extremely difficult for human developers to understand, spurring the need for effective WebAssembly reverse engineering techniques. In this paper, we propose StackSight, a novel neurosymbolic approach that combines Large Language Models (LLMs) with advanced program analysis to decompile complex WebAssembly code into readable C++ snippets. StackSight visualizes and tracks virtual stack alterations via a static analysis algorithm and then applies chain-of-thought prompting to harness LLM's complex reasoning capabilities. Evaluation results show that StackSight significantly improves WebAssembly decompilation. Our user study also demonstrates that code snippets generated by StackSight have significantly higher win rates and enable a better grasp of code semantics.

Deep Learning · Robustness

Sara Ahmadian, Edith Cohen

Cardinality sketches are popular data structures that enhance the efficiency of working with large data sets. The sketches are randomized representations of sets that are only of logarithmic size but can support set merges and approximate cardinality (i.e., distinct count) queries. When queries are not adaptive, that is, they do not depend on preceding query responses, the design provides strong guarantees of correctly answering a number of queries exponential in the sketch size $k$. In this work, we investigate the performance of cardinality sketches in adaptive settings and unveil inherent vulnerabilities. We design an attack against the ``standard'' estimators that constructs an adversarial input by post-processing responses to a set of simple non-adaptive queries of size linear in the sketch size $k$. Empirically, our attack used only $4k$ queries with the widely used HyperLogLog (HLL++) Flajolet et al., 2007; Heule et al., 2013) sketch. The simple attack technique suggests it can be effective with post-processed natural workloads. Finally and importantly, we demonstrate that the vulnerability is inherent as any estimator applied to known sketch structures can be attacked using a number of queries that is quadratic in $k$, matching a generic upper bound.

Miscellaneous Aspects of Machine Learning · Sequential, Network, and Time Series Modeling

Christoph Jürgen Hemmer, Manuel Brenner, Florian Hess, Daniel Durstewitz

In dynamical systems reconstruction (DSR) we seek to infer from time series measurements a generative model of the underlying dynamical process. This is a prime objective in any scientific discipline, where we are particularly interested in parsimonious models with a low parameter load. A common strategy here is parameter pruning, removing all parameters with small weights. However, here we find this strategy does not work for DSR, where even low magnitude parameters can contribute considerably to the system dynamics. On the other hand, it is well known that many natural systems which generate complex dynamics, like the brain or ecological networks, have a sparse topology with comparatively few links. Inspired by this, we show that *geometric pruning*, where in contrast to magnitude-based pruning weights with a low contribution to an attractor's geometrical structure are removed, indeed manages to reduce parameter load substantially without significantly hampering DSR quality. We further find that the networks resulting from geometric pruning have a specific type of topology, and that this topology, and not the magnitude of weights, is what is most crucial to performance. We provide an algorithm that automatically generates such topologies which can be used as priors for generative modeling of dynamical systems by RNNs, and compare it to other well studied topologies like small-world or scale-free networks.

Reinforcement Learning

Harrison Lee, Samrat Phatale, Hassan Mansoor, Thomas Mesnard, Johan Ferret, Kellie Lu, Colton Bishop, Ethan Hall, Victor Carbune, Abhinav Rastogi 等

Reinforcement learning from human feedback (RLHF) has proven effective in aligning large language models (LLMs) with human preferences, but gathering high-quality preference labels is expensive. RL from AI Feedback (RLAIF), introduced in Bai et al. (2022b), offers a promising alternative that trains the reward model (RM) on preferences generated by an off-the-shelf LLM. Across the tasks of summarization, helpful dialogue generation, and harmless dialogue generation, we show that RLAIF achieves comparable performance to RLHF. Furthermore, we take a step towards "self-improvement" by demonstrating that RLAIF can outperform a supervised fine-tuned baseline even when the AI labeler is the same size as the policy, or even the exact same checkpoint as the initial policy. Finally, we introduce direct-RLAIF (d-RLAIF) - a technique that circumvents RM training by obtaining rewards directly from an off-the-shelf LLM during RL, which achieves superior performance to canonical RLAIF. Our results suggest that RLAIF can achieve performance on-par with using human feedback, offering a potential solution to the scalability limitations of RLHF.

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

Xi Han, Fei Hou, Hong Qin

Numerical solvers of Partial Differential Equations (PDEs) are of fundamental significance to science and engineering. To date, the historical reliance on legacy techniques has circumscribed possible integration of big data knowledge and exhibits sub-optimal efficiency for certain PDE formulations, while data-driven neural methods typically lack mathematical guarantee of convergence and correctness. This paper articulates a mathematically rigorous neural solver for linear PDEs. The proposed UGrid solver, built upon the principled integration of U-Net and MultiGrid, manifests a mathematically rigorous proof of both convergence and correctness, and showcases high numerical accuracy, as well as strong generalization power to various input geometry/values and multiple PDE formulations. In addition, we devise a new residual loss metric, which enables unsupervised training and affords more stability and a larger solution space over the legacy losses.

Social Aspects · Accountability, Transparency and Interpretability

Tom Bewley, Salim I. Amoukou, Saumitra Mishra, Daniele Magazzeni, Manuela Veloso

We introduce **T-CREx**, a novel model-agnostic method for local and global counterfactual explanation (CE), which summarises recourse options for both individuals and groups in the form of generalised rules. It leverages tree-based surrogate models to learn the counterfactual rules, alongside *metarules* denoting their regimes of optimality, providing both a global analysis of model behaviour and diverse recourse options for users. Experiments indicate that **T-CREx** achieves superior aggregate performance over existing rule-based baselines on a range of CE desiderata, while being orders of magnitude faster to run.

Deep Learning · Large Language Models

Long Qian, Juncheng Li, Yu Wu, Yaobo Ye, Hao Fei, Tat-Seng Chua, Yueting Zhuang, Siliang Tang

Large Language Models (LLMs) demonstrate remarkable proficiency in comprehending and handling text-based tasks. Many efforts are being made to transfer these attributes to video modality, which are termed Video-LLMs. However, existing Video-LLMs can only capture the coarse-grained semantics and are unable to effectively handle tasks related to comprehension or localization of specific video segments. In light of these challenges, we propose Momentor, a Video-LLM capable of accomplishing fine-grained temporal understanding tasks. To support the training of Momentor, we design an automatic data generation engine to construct Moment-10M, a large-scale video instruction dataset with segment-level instruction data. We train Momentor on Moment-10M, enabling it to perform segment-level reasoning and localization. Zero-shot evaluations on several tasks demonstrate that Momentor excels in fine-grained temporally grounded comprehension and localization.

Optimization · Bilevel optimization

Han Shen, Zhuoran Yang, Tianyi Chen

Bilevel optimization has been recently applied to many machine learning tasks. However, their applications have been restricted to the supervised learning setting, where static objective functions with benign structures are considered. But bilevel problems such as incentive design, inverse reinforcement learning (RL), and RL from human feedback (RLHF) are often modeled as dynamic objective functions that go beyond the simple static objective structures, which pose significant challenges of using existing bilevel solutions. To tackle this new class of bilevel problems, we introduce the first principled algorithmic framework for solving bilevel RL problems through the lens of penalty formulation. We provide theoretical studies of the problem landscape and its penalty-based (policy) gradient algorithms. We demonstrate the effectiveness of our algorithms via simulations in the Stackelberg game and RLHF.

Theory · Probabilistic Methods

Viktor Nilsson, Anirban Samaddar, Sandeep Madireddy, Pierre Nyquist

Information theoretic quantities play a central role in machine learning. The recent surge in the complexity of data and models has increased the demand for accurate estimation of these quantities. However, as the dimension grows the estimation presents significant challenges, with existing methods struggling already in relatively low dimensions. To address this issue, in this work, we introduce REMEDI for efficient and accurate estimation of differential entropy, a fundamental information theoretic quantity. The approach combines the minimization of the cross-entropy for simple, adaptive base models and the estimation of their deviation, in terms of the relative entropy, from the data density. Our approach demonstrates improvement across a broad spectrum of estimation tasks, encompassing entropy estimation on both synthetic and natural data. Further, we extend important theoretical consistency results to a more generalized setting required by our approach. We illustrate how the framework can be naturally extended to information theoretic supervised learning models, with a specific focus on the Information Bottleneck approach. It is demonstrated that the method delivers better accuracy compared to the existing methods in Information Bottleneck. In addition, we explore a natural connection between REMEDI and generative modeling using rejection sampling and Langevin dynamics.

Deep Learning · Theory

Flavio Martinelli, Berfin Simsek, Wulfram Gerstner, Johanni Brea

Can we identify the weights of a neural network by probing its input-output mapping? At first glance, this problem seems to have many solutions because of permutation, overparameterisation and activation function symmetries. Yet, we show that the incoming weight vector of each neuron is identifiable up to sign or scaling, depending on the activation function. Our novel method 'Expand-and-Cluster’ can identify layer sizes and weights of a target network for all commonly used activation functions. Expand-and-Cluster consists of two phases: (i) to relax the non-convex optimisation problem, we train multiple overparameterised student networks to best imitate the target function; (ii) to reverse engineer the target network's weights, we employ an ad-hoc clustering procedure that reveals the learnt weight vectors shared between students -- these correspond to the target weight vectors. We demonstrate successful weights and size recovery of trained shallow and deep networks with less than 10% overhead in the layer size and describe an 'ease-of-identifiability' axis by analysing 150 synthetic problems of variable difficulty.

Applications · Neuroscience, Cognitive Science

Nianzu Yang, Kaipeng Zeng, Haotian Lu, Yexin Wu, Zexin Yuan, Danni Chen, Shengdian Jiang, Jiaxiang Wu, Yimin Wang, Junchi Yan

Neuronal morphology is essential for studying brain functioning and understanding neurodegenerative disorders. As acquiring real-world morphology data is expensive, computational approaches for morphology generation have been studied. Traditional methods heavily rely on expert-set rules and parameter tuning, making it difficult to generalize across different types of morphologies. Recently, MorphVAE was introduced as the sole learning-based method, but its generated morphologies lack plausibility, i.e., they do not appear realistic enough and most of the generated samples are topologically invalid. To fill this gap, this paper proposes **MorphGrower**, which mimicks the neuron natural growth mechanism for generation. Specifically, MorphGrower generates morphologies layer by layer, with each subsequent layer conditioned on the previously generated structure. During each layer generation, MorphGrower utilizes a pair of sibling branches as the basic generation block and generates branch pairs synchronously. This approach ensures topological validity and allows for fine-grained generation, thereby enhancing the realism of the final generated morphologies. Results on four real-world datasets demonstrate that MorphGrower outperforms MorphVAE by a notable margin. Importantly, the electrophysiological response simulation demonstrates the plausibility of our generated samples from a neuroscience perspective. Our code is available at [https://github.com/Thinklab-SJTU/MorphGrower](https://github.com/Thinklab-SJTU/MorphGrower).

Social Aspects · Privacy-preserving Statistics and Machine Learning

Naman Agarwal, Satyen Kale, Karan Singh, Abhradeep Guha Thakurta

We design differentially private regret-minimizing algorithms in the online convex optimization (OCO) framework. Unlike recent results, our algorithms and analyses do not require smoothness, thus yielding the first private regret bounds with an optimal leading-order term for non-smooth loss functions. Additionally, even for smooth losses, the resulting regret guarantees improve upon previous results in terms their dependence of dimension. Our results provide the best known rates for DP-OCO in all practical regimes of the privacy parameter, barring when it is exceptionally small. The principal innovation in our algorithm design is the use of sampling from strongly log-concave densities which satisfy the Log-Sobolev Inequality. The resulting concentration of measure allows us to obtain a better trade-off for the dimension factors than prior work, leading to improved results. Following previous works on DP-OCO, the proposed algorithm explicitly limits the number of switches via rejection sampling. Thus, independently of privacy constraints, the algorithm also provides improved results for online convex optimization with a switching budget.

Deep Learning · Generative Models and Autoencoders

Shentao Yang, Tianqi Chen, Mingyuan Zhou

Aligning text-to-image diffusion model (T2I) with preference has been gaining increasing research attention. While prior works exist on directly optimizing T2I by preference data, these methods are developed under the bandit assumption of a latent reward on the entire diffusion reverse chain, while ignoring the sequential nature of the generation process. This may harm the efficacy and efficiency of preference alignment. In this paper, we take on a finer dense reward perspective and derive a tractable alignment objective that emphasizes the initial steps of the T2I reverse chain. In particular, we introduce temporal discounting into DPO-style explicit-reward-free objectives, to break the temporal symmetry therein and suit the T2I generation hierarchy. In experiments on single and multiple prompt generation, our method is competitive with strong relevant baselines, both quantitatively and qualitatively. Further investigations are conducted to illustrate the insight of our approach. Source code is available at https://github.com/Shentao-YANG/Dense_Reward_T2I .

Applications · Time Series

Benjamin Walker, Andrew McLeod, Tiexin QIN, Yichuan Cheng, Haoliang Li, Terry Lyons

The vector field of a controlled differential equation (CDE) describes the relationship between a *control* path and the evolution of a *solution* path. Neural CDEs (NCDEs) treat time series data as observations from a control path, parameterise a CDE's vector field using a neural network, and use the solution path as a continuously evolving hidden state. As their formulation makes them robust to irregular sampling rates, NCDEs are a powerful approach for modelling real-world data. Building on neural rough differential equations (NRDEs), we introduce Log-NCDEs, a novel, effective, and efficient method for training NCDEs. The core component of Log-NCDEs is the Log-ODE method, a tool from the study of rough paths for approximating a CDE's solution. Log-NCDEs are shown to outperform NCDEs, NRDEs, the linear recurrent unit, S5, and MAMBA on a range of multivariate time series datasets with up to $50{,}000$ observations.

Social Aspects · Privacy-preserving Statistics and Machine Learning

Xenia Heilmann, Mattia Cerrato, Ernst Althaus

Differentially private ML approaches seek to learn models which may be publicly released while guaranteeing that the input data is kept private. One issue with this construction is that further model releases based on the same training data (e.g. for a new task) incur a further privacy budget cost. Privacy-preserving synthetic data generation is one possible solution to this conundrum. However, models trained on synthetic private data struggle to approach the performance of private, ad-hoc models. In this paper, we present a novel method based on sum-product networks that is able to perform both privacy-preserving classification and privacy-preserving data generation with a single model. To the best of our knowledge, ours is the first approach that provides both discriminative and generative capabilities to differentially private ML. We show that our approach outperforms the state of the art in terms of stability (i.e. number of training runs required for convergence) and utility of the generated data.

Applications · Health

Andrew Song, Richard Chen, Guillaume Jaume, Anurag Vaidya, Alexander Baras, Faisal Mahmood

Multimodal survival methods combining gigapixel histology whole-slide images (WSIs) and transcriptomic profiles are particularly promising for patient prognostication and stratification. Current approaches involve tokenizing the WSIs into smaller patches ($>10^4$ patches) and transcriptomics into gene groups, which are then integrated using a Transformer for predicting outcomes. However, this process generates many tokens, which leads to high memory requirements for computing attention and complicates post-hoc interpretability analyses. Instead, we hypothesize that we can: (1) effectively summarize the morphological content of a WSI by condensing its constituting tokens using morphological prototypes, achieving more than $300\times$ compression; and (2) accurately characterize cellular functions by encoding the transcriptomic profile with biological pathway prototypes, all in an unsupervised fashion. The resulting multimodal tokens are then processed by a fusion network, either with a Transformer or an optimal transport cross-alignment, which now operates with a small and fixed number of tokens without approximations. Extensive evaluation on six cancer types shows that our framework outperforms state-of-the-art methods with much less computation while unlocking new interpretability analyses. The code is available at https://github.com/mahmoodlab/MMP.

Miscellaneous Aspects of Machine Learning · Online Learning, Active Learning and Bandits

Filippo Leveni, Guilherme Weigert Cassales, Bernhard Pfahringer, Albert Bifet, Giacomo Boracchi

The anomaly detection literature is abundant with offline methods, which require repeated access to data in memory, and impose impractical assumptions when applied to a streaming context. Existing online anomaly detection methods also generally fail to address these constraints, resorting to periodic retraining to adapt to the online context. We propose Online-iForest, a novel method explicitly designed for streaming conditions that seamlessly tracks the data generating process as it evolves over time. Experimental validation on real-world datasets demonstrated that Online-iForest is on par with online alternatives and closely rivals state-of-the-art offline anomaly detection techniques that undergo periodic retraining. Notably, Online-iForest consistently outperforms all competitors in terms of efficiency, making it a promising solution in applications where fast identification of anomalies is of primary importance such as cybersecurity, fraud and fault detection.