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Computational Biology

Gengmo Zhou, Zhen Wang, Feng Yu, Guolin Ke, Zhewei Wei, Zhifeng Gao

Virtual Screening is an essential technique in the early phases of drug discovery, aimed at identifying promising drug candidates from vast molecular libraries. Recently, ligand-based virtual screening has garnered significant attention due to its efficacy in conducting extensive database screenings without relying on specific protein-binding site information.Obtaining binding affinity data for complexes is highly expensive, resulting in a limited amount of available data that covers a relatively small chemical space. Moreover, these datasets contain a significant amount of inconsistent noise. It is challenging to identify an inductive bias that consistently maintains the integrity of molecular activity during data augmentation. To tackle these challenges, we propose S-MolSearch, the first framework to our knowledge, that leverages molecular 3D information and affinity information in semi-supervised contrastive learning for ligand-based virtual screening. % S-MolSearch processes both labeled and unlabeled data, trains molecular structural encoders, and generates soft labels for unlabeled data, drawing on the principles of inverse optimal transport.Drawing on the principles of inverse optimal transport, S-MolSearch efficiently processes both labeled and unlabeled data, training molecular structural encoders while generating soft labels for the unlabeled data.This design allows S-MolSearch to adaptively utilize unlabeled data within the learning process.Empirically, S-MolSearch demonstrates superior performance on widely-used benchmarks LIT-PCBA and DUD-E. It surpasses both structure-based and ligand-based virtual screening methods for AUROC, BEDROC and EF.

Fairness

Joachim Baumann, Celestine Mendler-Dünner

We investigate algorithmic collective action in transformer-based recommender systems. Our use case is a collective of fans aiming to promote the visibility of an underrepresented artist by strategically placing one of their songs in the existing playlists they control. We introduce two easily implementable strategies to select the position at which to insert the song and boost recommendations at test time. The strategies exploit statistical properties of the learner to leverage discontinuities in the recommendations, and the long-tail nature of song distributions. We evaluate the efficacy of our strategies using a publicly available recommender system model released by a major music streaming platform. Our findings reveal that even small collectives (controlling less than 0.01\% of the training data) can achieve up to $40\times$ more test time recommendations than songs with similar training set occurrences, on average. Focusing on the externalities of the strategy, we find that the recommendations of other songs are largely preserved, and the newly gained recommendations are distributed across various artists. Together, our findings demonstrate how carefully designed collective action strategies can be effective while not necessarily being adversarial.

Reinforcement Learning · Batch Offline

Sili Huang, Jifeng Hu, Zhejian Yang, Liwei Yang, Tao Luo, Hechang Chen, Lichao Sun, Bo Yang

Recent works have shown the remarkable superiority of transformer models in reinforcement learning (RL), where the decision-making problem is formulated as sequential generation. Transformer-based agents could emerge with self-improvement in online environments by providing task contexts, such as multiple trajectories, called in-context RL. However, due to the quadratic computation complexity of attention in transformers, current in-context RL methods suffer from huge computational costs as the task horizon increases. In contrast, the Mamba model is renowned for its efficient ability to process long-term dependencies, which provides an opportunity for in-context RL to solve tasks that require long-term memory. To this end, we first implement Decision Mamba (DM) by replacing the backbone of Decision Transformer (DT). Then, we propose a Decision Mamba-Hybrid (DM-H) with the merits of transformers and Mamba in high-quality prediction and long-term memory. Specifically, DM-H first generates high-value sub-goals from long-term memory through the Mamba model. Then, we use sub-goals to prompt the transformer, establishing high-quality predictions. Experimental results demonstrate that DM-H achieves state-of-the-art in long and short-term tasks, such as D4RL, Grid World, and Tmaze benchmarks. Regarding efficiency, the online testing of DM-H in the long-term task is 28$\times$ times faster than the transformer-based baselines.

Multimodal Models

Bhavika Devnani, Skyler Seto, Zakaria Aldeneh, Alessandro Toso, Elena Menyaylenko, Barry-John Theobald, Jonathan Sheaffer, Miguel Sarabia

Humans can picture a sound scene given an imprecise natural language description. For example, it is easy to imagine an acoustic environment given a phrase like "the lion roar came from right behind me!". For a machine to have the same degree of comprehension, the machine must know what a lion is (semantic attribute), what the concept of "behind" is (spatial attribute) and how these pieces of linguistic information align with the semantic and spatial attributes of the sound (what a roar sounds like when its coming from behind). State-of-the-art audio foundation models, such as CLAP, which learn to map between audio scenes and natural textual descriptions, are trained on non-spatial audio and text pairs, and hence lack spatial awareness. In contrast, sound event localization and detection models are limited to recognizing sounds from a fixed number of classes, and they localize the source to absolute position (e.g., 0.2m) rather than a position described using natural language (e.g., "next to me"). To address these gaps, we present ELSA (Embeddings for Language and Spatial Audio), a spatially aware-audio and text embedding model trained using multimodal contrastive learning. ELSA supports non-spatial audio, spatial audio, and open vocabulary text captions describing both the spatial and semantic components of sound. To train ELSA: (a) we spatially augment the audio and captions of three open-source audio datasets totaling 4,738 hours and 890,038 samples of audio comprised from 8,972 simulated spatial configurations, and (b) we design an encoder to capture the semantics of non-spatial audio, and the semantics and spatial attributes of spatial audio using contrastive learning. ELSA is a single model that is competitive with state-of-the-art for both semantic retrieval and 3D source localization. In particular, ELSA achieves +2.8\% mean audio-to-text and text-to-audio R@1 above the LAION-CLAP baseline, and outperforms by -11.6° mean-absolute-error in 3D source localization over the SeldNET baseline on the TUT Sound Events 2018 benchmark. Moreover, we show that the representation-space of ELSA is structured, enabling swapping of direction of audio via vector arithmetic of two directional text embeddings.

Generative Models

Tobias Schröder, Zijing Ou, Yingzhen Li, Andrew Duncan

Energy-based models (EBMs) offer a flexible framework for probabilistic modelling across various data domains. However, training EBMs on data in discrete or mixed state spaces poses significant challenges due to the lack of robust and fast sampling methods. In this work, we propose to train discrete EBMs with Energy Discrepancy, a loss function which only requires the evaluation of the energy function at data points and their perturbed counterparts, thus eliminating the need for Markov chain Monte Carlo. We introduce perturbations of the data distribution by simulating a diffusion process on the discrete state space endowed with a graph structure. This allows us to inform the choice of perturbation from the structure of the modelled discrete variable, while the continuous time parameter enables fine-grained control of the perturbation. Empirically, we demonstrate the efficacy of the proposed approaches in a wide range of applications, including the estimation of discrete densities with non-binary vocabulary and binary image modelling. We also introduce the first application of EBMs to tabular data sets with applications in synthetic data generation and calibrated classification.

Trustworthy Machine Learning

Geng Yu, Jianing Zhu, Jiangchao Yao, Bo Han

Out-of-distribution (OOD) detection is crucial for deploying reliable machine learning models in open-world applications. Recent advances in CLIP-based OOD detection have shown promising results via regularizing prompt tuning with OOD features extracted from ID data. However, the irrelevant context mined from ID data can be spurious due to the inaccurate foreground-background decomposition, thus limiting the OOD detection performance. In this work, we propose a novel framework, namely, \textit{Self-Calibrated Tuning (SCT)}, to mitigate this problem for effective OOD detection with only the given few-shot ID data. Specifically, SCT introduces modulating factors respectively on the two components of the original learning objective. It adaptively directs the optimization process between the two tasks during training on data with different prediction uncertainty to calibrate the influence of OOD regularization, which is compatible with many prompt tuning based OOD detection methods. Extensive experiments and analyses have been conducted to characterize and demonstrate the effectiveness of the proposed SCT. The code is publicly available at: https://github.com/tmlr-group/SCT.

Causality

Chenxi Liu, Yongqiang Chen, Tongliang Liu, Mingming Gong, James Cheng, Bo Han, Kun Zhang

Revealing the underlying causal mechanisms in the real world is the key to the development of science. Despite the progress in the past decades, traditional causal discovery approaches (CDs) mainly rely on high-quality measured variables, usually given by human experts, to find causal relations. The lack of well-defined high-level variables in many real-world applications has already been a longstanding roadblock to a broader application of CDs. To this end, this paper presents Causal representatiOn AssistanT (COAT) that introduces large language models (LLMs) to bridge the gap. LLMs are trained on massive observations of the world and have demonstrated great capability in extracting key information from unstructured data. Therefore, it is natural to employ LLMs to assist with proposing useful high-level factors and crafting their measurements. Meanwhile, COAT also adopts CDs to find causal relations among the identified variables as well as to provide feedback to LLMs to iteratively refine the proposed factors. We show that LLMs and CDs are mutually beneficial and the constructed feedback provably also helps with the factor proposal. We construct and curate several synthetic and real-world benchmarks including analysis of human reviews and diagnosis of neuropathic and brain tumors, to comprehensively evaluate COAT. Extensive empirical results confirm the effectiveness and reliability of COAT with significant improvements.

Generative Models · Reasoning

Tengxiao Liu, Qipeng Guo, Xiangkun Hu, Cheng Jiayang, Yue Zhang, Xipeng Qiu, Zheng Zhang

Trained on vast corpora of human language, language models demonstrate emergent human-like reasoning abilities. Yet they are still far from true intelligence, which opens up intriguing opportunities to explore the parallels of humans and model behaviors. In this work, we study the ability to skip steps in reasoning—a hallmark of human expertise developed through practice. Unlike humans, who may skip steps to enhance efficiency or to reduce cognitive load, models do not inherently possess such motivations to minimize reasoning steps. To address this, we introduce a controlled framework that stimulates step-skipping behavior by iteratively refining models to generate shorter and accurate reasoning paths. Empirical results indicate that models can develop the step skipping ability under our guidance. Moreover, after fine-tuning on expanded datasets that include both complete and skipped reasoning sequences, the models can not only resolve tasks with increased efficiency without sacrificing accuracy, but also exhibit comparable and even enhanced generalization capabilities in out-of-domain scenarios. Our work presents the first exploration into human-like step-skipping ability and provides fresh perspectives on how such cognitive abilities can benefit AI models.

Probabilistic Methods

Jiajie Tao, Hao Ni, Chong Liu

Since the weak convergence for stochastic processes does not account for the growth of information over time which is represented by the underlying filtration, a slightly erroneous stochastic model in weak topology may cause huge loss in multi-periods decision making problems. To address such discontinuities, Aldous introduced the extended weak convergence, which can fully characterise all essential properties, including the filtration, of stochastic processes; however, it was considered to be hard to find efficient numerical implementations. In this paper, we introduce a novel metric called High Rank PCF Distance (HRPCFD) for extended weak convergence based on the high rank path development method from rough path theory, which also defines the characteristic function for measure-valued processes. We then show that such HRPCFD admits many favourable analytic properties which allows us to design an efficient algorithm for training HRPCFD from data and construct the HRPCF-GAN by using HRPCFD as the discriminator for conditional time series generation. Our numerical experiments on both hypothesis testing and generative modelling validate the out-performance of our approach compared with several state-of-the-art methods, highlighting its potential in broad applications of synthetic time series generation and in addressing classic financial and economic challenges, such as optimal stopping or utility maximisation problems. Code is available at https://github.com/DeepIntoStreams/High-Rank-PCF-GAN.git.

Trustworthy Machine Learning

JIAAN LUO, Feng Hong, Jiangchao Yao, Bo Han, Ya Zhang, Yanfeng Wang

In deep learning, model performance often deteriorates when trained on highly imbalanced datasets, especially when evaluation metrics require robust generalization across underrepresented classes. To address the challenges posed by imbalanced data distributions, this study introduces a novel method utilizing density ratio estimation for dynamic class weight adjustment, termed as Re-weighting with Density Ratio (RDR). Our method adaptively adjusts the importance of each class during training, mitigates overfitting on dominant classes and enhances model adaptability across diverse datasets. Extensive experiments conducted on various large scale benchmark datasets validate the effectiveness of our method. Results demonstrate substantial improvements in generalization capabilities, particularly under severely imbalanced conditions.

Deep Learning · Theory

Daniel Beaglehole, Peter Súkeník, Marco Mondelli, Misha Belkin

Deep Neural Collapse (DNC) refers to the surprisingly rigid structure of the data representations in the final layers of Deep Neural Networks (DNNs). Though the phenomenon has been measured in a variety of settings, its emergence is typically explained via data-agnostic approaches, such as the unconstrained features model. In this work, we introduce a data-dependent setting where DNC forms due to feature learning through the average gradient outer product (AGOP). The AGOP is defined with respect to a learned predictor and is equal to the uncentered covariance matrix of its input-output gradients averaged over the training dataset. Deep Recursive Feature Machines are a method that constructs a neural network by iteratively mapping the data with the AGOP and applying an untrained random feature map. We demonstrate theoretically and empirically that DNC occurs in Deep Recursive Feature Machines as a consequence of the projection with the AGOP matrix computed at each layer. We then provide evidence that this mechanism holds for neural networks more generally. We show that the right singular vectors and values of the weights can be responsible for the majority of within-class variability collapse for DNNs trained in the feature learning regime. As observed in recent work, this singular structure is highly correlated with that of the AGOP.

Computer Vision · Segmentation

Laurynas Karazija, Iro Laina, Christian Rupprecht, Andrea Vedaldi

We consider the problem of segmenting objects in videos based on their motion and no other forms of supervision. Prior work has often approached this problem by using the principle of common fate, namely the fact that the motion of points that belong to the same object is strongly correlated. However, most authors have only considered instantaneous motion from optical flow. In this work, we present a way to train a segmentation network using long-term point trajectories as a supervisory signal to complement optical flow. The key difficulty is that long-term motion, unlike instantaneous motion, is difficult to model -- any parametric approximation is unlikely to capture complex motion patterns over long periods of time. We instead draw inspiration from subspace clustering approaches, proposing a loss function that seeks to group the trajectories into low-rank matrices where the motion of object points can be approximately explained as a linear combination of other point tracks. Our method outperforms the prior art on motion-based segmentation, which shows the utility of long-term motion and the effectiveness of our formulation.

Trustworthy Machine Learning

Jialiang Wang, Xiong Zhou, Deming Zhai, Junjun Jiang, Xiangyang Ji, Xianming Liu

Noisy labels pose a common challenge for training accurate deep neural networks. To mitigate label noise, prior studies have proposed various robust loss functions to achieve noise tolerance in the presence of label noise, particularly symmetric losses. However, they usually suffer from the underfitting issue due to the overly strict symmetric condition. In this work, we propose a simple yet effective approach for relaxing the symmetric condition, namely **$\epsilon$-softmax**, which simply modifies the outputs of the softmax layer to approximate one-hot vectors with a controllable error $\epsilon$. Essentially, ***$\epsilon$-softmax** not only acts as an alternative for the softmax layer, but also implicitly plays the crucial role in modifying the loss function.* We prove theoretically that **$\epsilon$-softmax** can achieve noise-tolerant learning with controllable excess risk bound for almost any loss function. Recognizing that **$\epsilon$-softmax**-enhanced losses may slightly reduce fitting ability on clean datasets, we further incorporate them with one symmetric loss, thereby achieving a better trade-off between robustness and effective learning. Extensive experiments demonstrate the superiority of our method in mitigating synthetic and real-world label noise.

Computer Vision

Jikang Cheng, Zhiyuan Yan, Ying Zhang, Yuhao Luo, Zhongyuan Wang, Chen Li

The generalization ability of deepfake detectors is vital for their applications in real-world scenarios. One effective solution to enhance this ability is to train the models with manually-blended data, which we termed ''blendfake'', encouraging models to learn generic forgery artifacts like blending boundary. Interestingly, current SoTA methods utilize blendfake $\textit{without}$ incorporating any deepfake data in their training process. This is likely because previous empirical observations suggest that vanilla hybrid training (VHT), which combines deepfake and blendfake data, results in inferior performance to methods using only blendfake data (so-called "1+1<2"). Therefore, a critical question arises: Can we leave deepfake behind and rely solely on blendfake data to train an effective deepfake detector? Intuitively, as deepfakes also contain additional informative forgery clues ($\textit{e.g.,}$ deep generative artifacts), excluding all deepfake data in training deepfake detectors seems counter-intuitive. In this paper, we rethink the role of blendfake in detecting deepfakes and formulate the process from "real to blendfake to deepfake" to be a $\textit{progressive transition}$. Specifically, blendfake and deepfake can be explicitly delineated as the oriented pivot anchors between "real-to-fake" transitions. The accumulation of forgery information should be oriented and progressively increasing during this transition process. To this end, we propose an $\underline{O}$riented $\underline{P}$rogressive $\underline{R}$egularizor (OPR) to establish the constraints that compel the distribution of anchors to be discretely arranged. Furthermore, we introduce feature bridging to facilitate the smooth transition between adjacent anchors. Extensive experiments confirm that our design allows leveraging forgery information from both blendfake and deepfake effectively and comprehensively. Code is available at https://github.com/beautyremain/ProDet.

Robotics

Zichen Cui, Hengkai Pan, Aadhithya Iyer, Siddhant Haldar, Lerrel Pinto

Imitation learning has proven to be a powerful tool for training complex visuo-motor policies. However, current methods often require hundreds to thousands of expert demonstrations to handle high-dimensional visual observations. A key reason for this poor data efficiency is that visual representations are predominantly either pretrained on out-of-domain data or trained directly through a behavior cloning objective. In this work, we present DynaMo, a new in-domain, self-supervised method for learning visual representations. Given a set of expert demonstrations, we jointly learn a latent inverse dynamics model and a forward dynamics model over a sequence of image embeddings, predicting the next frame in latent space, without augmentations, contrastive sampling, or access to ground truth actions. Importantly, DynaMo does not require any out-of-domain data such as Internet datasets or cross-embodied datasets. On a suite of six simulated and real environments, we show that representations learned with DynaMo significantly improve downstream imitation learning performance over prior self-supervised learning objectives, and pretrained representations. Gains from using DynaMo hold across policy classes such as Behavior Transformer, Diffusion Policy, MLP, and nearest neighbors. Finally, we ablate over key components of DynaMo and measure its impact on downstream policy performance. Robot videos are best viewed at https://dynamo-ssl.github.io.

Reinforcement Learning · Deep RL

Steven Li, Rickmer Krohn, Tao Chen, Anurag Ajay, Pulkit Agrawal, Georgia Chalvatzaki

Deep reinforcement learning (RL) algorithms typically parameterize the policy as a deep network that outputs either a deterministic action or a stochastic one modeled as a Gaussian distribution, hence restricting learning to a single behavioral mode. Meanwhile, diffusion models emerged as a powerful framework for multimodal learning. However, the use of diffusion policies in online RL is hindered by the intractability of policy likelihood approximation, as well as the greedy objective of RL methods that can easily skew the policy to a single mode. This paper presents Deep Diffusion Policy Gradient (DDiffPG), a novel actor-critic algorithm that learns from scratch multimodal policies parameterized as diffusion models while discovering and maintaining versatile behaviors. DDiffPG explores and discovers multiple modes through off-the-shelf unsupervised clustering combined with novelty-based intrinsic motivation. DDiffPG forms a multimodal training batch and utilizes mode-specific Q-learning to mitigate the inherent greediness of the RL objective, ensuring the improvement of the diffusion policy across all modes. Our approach further allows the policy to be conditioned on mode-specific embeddings to explicitly control the learned modes. Empirical studies validate DDiffPG's capability to master multimodal behaviors in complex, high-dimensional continuous control tasks with sparse rewards, also showcasing proof-of-concept dynamic online replanning when navigating mazes with unseen obstacles. Our project page is available at https://supersglzc.github.io/projects/ddiffpg/.

Deep Learning · Representation Learning

Olaf Lipinski, Adam Sobey, Federico Cerutti, Timothy Norman

Effective communication requires the ability to refer to specific parts of an observation in relation to others. While emergent communication literature shows success in developing various language properties, no research has shown the emergence of such positional references. This paper demonstrates how agents can communicate about spatial relationships within their observations. The results indicate that agents can develop a language capable of expressing the relationships between parts of their observation, achieving over 90% accuracy when trained in a referential game which requires such communication. Using a collocation measure, we demonstrate how the agents create such references. This analysis suggests that agents use a mixture of non-compositional and compositional messages to convey spatial relationships. We also show that the emergent language is interpretable by humans. The translation accuracy is tested by communicating with the receiver agent, where the receiver achieves over 78% accuracy using parts of this lexicon, confirming that the interpretation of the emergent language was successful.

Trustworthy Machine Learning

Xiaomeng Hu, Pin-Yu Chen, Tsung-Yi Ho

Large Language Models (LLMs) are becoming a prominent generative AI tool, where the user enters a query and the LLM generates an answer. To reduce harm and misuse, efforts have been made to align these LLMs to human values using advanced training techniques such as Reinforcement Learning from Human Feedback (RLHF). However, recent studies have highlighted the vulnerability of LLMs to adversarial jailbreak attempts aiming at subverting the embedded safety guardrails. To address this challenge, this paper defines and investigates the **Refusal Loss** of LLMs and then proposes a method called **Gradient Cuff** to detect jailbreak attempts. Gradient Cuff exploits the unique properties observed in the refusal loss landscape, including functional values and its smoothness, to design an effective two-step detection strategy. Experimental results on two aligned LLMs (LLaMA-2-7B-Chat and Vicuna-7B-V1.5) and six types of jailbreak attacks (GCG, AutoDAN, PAIR, TAP, Base64, and LRL) show that Gradient Cuff can significantly improve the LLM's rejection capability for malicious jailbreak queries, while maintaining the model's performance for benign user queries by adjusting the detection threshold.

Chi-Chang Lee, Zhang-Wei Hong, Pulkit Agrawal

In many reinforcement learning (RL) applications, incorporating heuristic rewards alongside the task reward is crucial for achieving desirable performance. Heuristics encode prior human knowledge about how a task should be done, providing valuable hints for RL algorithms. However, such hints may not be optimal, limiting the performance of learned policies. The currently established way of using heuristics is to modify the heuristic reward in a manner that ensures that the optimal policy learned with it remains the same as the optimal policy for the task reward (i.e., optimal policy invariance). However, these methods often fail in practical scenarios with limited training data. We found that while optimal policy invariance ensures convergence to the best policy based on task rewards, it doesn't guarantee better performance than policies trained with biased heuristics under a finite data regime, which is impractical. In this paper, we introduce a new principle tailored for finite data settings. Instead of enforcing optimal policy invariance, we train a policy that combines task and heuristic rewards and ensures it outperforms the heuristic-trained policy. As such, we prevent policies from merely exploiting heuristic rewards without improving the task reward. Our experiments on robotic locomotion, helicopter control, and manipulation tasks demonstrate that our method consistently outperforms the heuristic policy, regardless of the heuristic rewards' quality.Code is available at https://github.com/Improbable-AI/hepo.

Trustworthy Machine Learning

Jiongli Zhu, Su Feng, Boris Glavic, Babak Salimi

We introduce an efficient method for learning linear models from uncertain data, where uncertainty is represented as a set of possible variations in the data, leading to predictive multiplicity. Our approach leverages abstract interpretation and zonotopes, a type of convex polytope, to compactly represent these dataset variations, enabling the symbolic execution of gradient descent on all possible worlds simultaneously. We develop techniques to ensure that this process converges to a fixed point and derive closed-form solutions for this fixed point. Our method provides sound over-approximations of all possible optimal models and viable prediction ranges. We demonstrate the effectiveness of our approach through theoretical and empirical analysis, highlighting its potential to reason about model and prediction uncertainty due to data quality issues in training data.