The ability to engineer novel proteins with higher fitness for a desired property would be revolutionary for biotechnology and medicine. Modeling the combinatorially large space of sequences is infeasible; prior methods often constrain optimization to a small mutational radius, but this drastically limits the design space. Instead of heuristics, we propose smoothing the fitness landscape to facilitate protein optimization. First, we formulate protein fitness as a graph signal then use Tikunov regularization to smooth the fitness landscape. We find optimizing in this smoothed landscape leads to improved performance across multiple methods in the GFP and AAV benchmarks. Second, we achieve state-of-the-art results utilizing discrete energy-based models and MCMC in the smoothed landscape. Our method, called Gibbs sampling with Graph-based Smoothing (GGS), demonstrates a unique ability to achieve 2.5 fold fitness improvement (with in-silico evaluation) over its training set. GGS demonstrates potential to optimize proteins in the limited data regime. Code: //github.com/kirjner/GGS
Recent advances in large language models (LLMs) have blurred the boundary of high-quality text generation between humans and machines, which is favorable for generative text steganography. While, current advanced steganographic mapping is not suitable for LLMs since most users are restricted to accessing only the black-box API or user interface of the LLMs, thereby lacking access to the training vocabulary and its sampling probabilities. In this paper, we explore a black-box generative text steganographic method based on the user interfaces of large language models, which is called LLM-Stega. The main goal of LLM-Stega is that the secure covert communication between Alice (sender) and Bob (receiver) is conducted by using the user interfaces of LLMs. Specifically, We first construct a keyword set and design a new encrypted steganographic mapping to embed secret messages. Furthermore, to guarantee accurate extraction of secret messages and rich semantics of generated stego texts, an optimization mechanism based on reject sampling is proposed. Comprehensive experiments demonstrate that the proposed LLM-Stega outperforms current state-of-the-art methods.
Human motion prediction and trajectory forecasting are essential in human motion analysis. Nowadays, sensors can be seamlessly integrated into clothing using cutting-edge electronic textile (e-textile) technology, allowing long-term recording of human movements outside the laboratory. Motivated by the recent findings that clothing-attached sensors can achieve higher activity recognition accuracy than body-attached sensors. This work investigates the performance of human motion prediction using clothing-attached sensors compared with body-attached sensors. It reports experiments in which statistical models learnt from the movement of loose clothing are used to predict motion patterns of the body of robotically simulated and real human behaviours. Counterintuitively, the results show that fabric-attached sensors can have better motion prediction performance than rigid-attached sensors. Specifically, The fabric-attached sensor can improve the accuracy up to 40% and requires up to 80% less duration of the past trajectory to achieve high prediction accuracy (i.e., 95%) compared to the rigid-attached sensor.
Continual learning has gained increasing importance as it facilitates the acquisition and refinement of scalable knowledge and skills in language models. However, existing methods typically encounter strict limitations and challenges in real-world scenarios, such as reliance on experience replay, optimization constraints, and inference task-ID. In this study, we introduce the Scalable Language Model (SLM) to overcome these limitations within a more challenging and generalized setting, representing a significant advancement toward practical applications for continual learning. Specifically, we propose the Joint Adaptive Re-Parameterization (JARe), integrated with Dynamic Task-related Knowledge Retrieval (DTKR), to enable adaptive adjustment of language models based on specific downstream tasks. This approach leverages the task distribution within the vector space, aiming to achieve a smooth and effortless continual learning process. Our method demonstrates state-of-the-art performance on diverse backbones and benchmarks, achieving effective continual learning in both full-set and few-shot scenarios with minimal forgetting. Moreover, while prior research primarily focused on a single task type such as classification, our study goes beyond, with the large language model, i.e., LLaMA-2, to explore the effects across diverse domains and task types, such that a single language model can be decently scaled to broader applications.
Instrumental variables (IVs) are a popular and powerful tool for estimating causal effects in the presence of unobserved confounding. However, classical approaches rely on strong assumptions such as the $\textit{exclusion criterion}$, which states that instrumental effects must be entirely mediated by treatments. This assumption often fails in practice. When IV methods are improperly applied to data that do not meet the exclusion criterion, estimated causal effects may be badly biased. In this work, we propose a novel solution that provides $\textit{partial}$ identification in linear models given a set of $\textit{leaky instruments}$, which are allowed to violate the exclusion criterion to some limited degree. We derive a convex optimization objective that provides provably sharp bounds on the average treatment effect under some common forms of information leakage, and implement inference procedures to quantify the uncertainty of resulting estimates. We demonstrate our method in a set of experiments with simulated data, where it performs favorably against the state of the art.
People rely on social skills like conflict resolution to communicate effectively and to thrive in both work and personal life. However, practice environments for social skills are typically out of reach for most people. How can we make social skill training more available, accessible, and inviting? Drawing upon interdisciplinary research from communication and psychology, this perspective paper identifies social skill barriers to enter specialized fields. Then we present a solution that leverages large language models for social skill training via a generic framework. Our AI Partner, AI Mentor framework merges experiential learning with realistic practice and tailored feedback. This work ultimately calls for cross-disciplinary innovation to address the broader implications for workforce development and social equality.
We envision 'AI scientists' as systems capable of skeptical learning and reasoning that empower biomedical research through collaborative agents that integrate machine learning tools with experimental platforms. Rather than taking humans out of the discovery process, biomedical AI agents combine human creativity and expertise with AI's ability to analyze large datasets, navigate hypothesis spaces, and execute repetitive tasks. AI agents are proficient in a variety of tasks, including self-assessment and planning of discovery workflows. These agents use large language models and generative models to feature structured memory for continual learning and use machine learning tools to incorporate scientific knowledge, biological principles, and theories. AI agents can impact areas ranging from hybrid cell simulation, programmable control of phenotypes, and the design of cellular circuits to the development of new therapies.
Image editing has been a long-standing challenge in the research community with its far-reaching impact on numerous applications. Recently, text-driven methods started to deliver promising results in domains like human faces, but their applications to more complex domains have been relatively limited. In this work, we explore the task of fashion style editing, where we aim to manipulate the fashion style of human imagery using text descriptions. Specifically, we leverage a generative human prior and achieve fashion style editing by navigating its learned latent space. We first verify that the existing text-driven editing methods fall short for our problem due to their overly simplified guidance signal, and propose two directions to reinforce the guidance: textual augmentation and visual referencing. Combined with our empirical findings on the latent space structure, our Fashion Style Editing framework (FaSE) successfully projects abstract fashion concepts onto human images and introduces exciting new applications to the field.
Noisy label learning aims to train deep neural networks using a large amount of samples with noisy labels, whose main challenge comes from how to deal with the inaccurate supervision caused by wrong labels. Existing works either take the label correction or sample selection paradigm to involve more samples with accurate labels into the training process. In this paper, we propose a simple yet effective sample selection algorithm, termed as Pairwise Similarity Distribution Clustering~(PSDC), to divide the training samples into one clean set and another noisy set, which can power any of the off-the-shelf semi-supervised learning regimes to further train networks for different downstream tasks. Specifically, we take the pairwise similarity between sample pairs to represent the sample structure, and the Gaussian Mixture Model~(GMM) to model the similarity distribution between sample pairs belonging to the same noisy cluster, therefore each sample can be confidently divided into the clean set or noisy set. Even under severe label noise rate, the resulting data partition mechanism has been proved to be more robust in judging the label confidence in both theory and practice. Experimental results on various benchmark datasets, such as CIFAR-10, CIFAR-100 and Clothing1M, demonstrate significant improvements over state-of-the-art methods.
Recently, graph neural networks (GNNs) have revolutionized the field of graph representation learning through effectively learned node embeddings, and achieved state-of-the-art results in tasks such as node classification and link prediction. However, current GNN methods are inherently flat and do not learn hierarchical representations of graphs---a limitation that is especially problematic for the task of graph classification, where the goal is to predict the label associated with an entire graph. Here we propose DiffPool, a differentiable graph pooling module that can generate hierarchical representations of graphs and can be combined with various graph neural network architectures in an end-to-end fashion. DiffPool learns a differentiable soft cluster assignment for nodes at each layer of a deep GNN, mapping nodes to a set of clusters, which then form the coarsened input for the next GNN layer. Our experimental results show that combining existing GNN methods with DiffPool yields an average improvement of 5-10% accuracy on graph classification benchmarks, compared to all existing pooling approaches, achieving a new state-of-the-art on four out of five benchmark data sets.
Deep neural networks (DNNs) have been found to be vulnerable to adversarial examples resulting from adding small-magnitude perturbations to inputs. Such adversarial examples can mislead DNNs to produce adversary-selected results. Different attack strategies have been proposed to generate adversarial examples, but how to produce them with high perceptual quality and more efficiently requires more research efforts. In this paper, we propose AdvGAN to generate adversarial examples with generative adversarial networks (GANs), which can learn and approximate the distribution of original instances. For AdvGAN, once the generator is trained, it can generate adversarial perturbations efficiently for any instance, so as to potentially accelerate adversarial training as defenses. We apply AdvGAN in both semi-whitebox and black-box attack settings. In semi-whitebox attacks, there is no need to access the original target model after the generator is trained, in contrast to traditional white-box attacks. In black-box attacks, we dynamically train a distilled model for the black-box model and optimize the generator accordingly. Adversarial examples generated by AdvGAN on different target models have high attack success rate under state-of-the-art defenses compared to other attacks. Our attack has placed the first with 92.76% accuracy on a public MNIST black-box attack challenge.