Yanchao Tan, Zihao Zhou, Hang Lv, Weiming Liu, Carl Yang
{"title":"WalkLM: A Uniform Language Model Fine-tuning Framework for Attributed Graph Embedding.","authors":"Yanchao Tan, Zihao Zhou, Hang Lv, Weiming Liu, Carl Yang","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>Graphs are widely used to model interconnected entities and improve downstream predictions in various real-world applications. However, real-world graphs nowadays are often associated with complex attributes on multiple types of nodes and even links that are hard to model uniformly, while the widely used graph neural networks (GNNs) often require sufficient training toward specific downstream predictions to achieve strong performance. In this work, we take a fundamentally different approach than GNNs, to simultaneously achieve deep joint modeling of complex attributes and flexible structures of real-world graphs and obtain unsupervised generic graph representations that are not limited to specific downstream predictions. Our framework, built on a natural integration of language models (LMs) and random walks (RWs), is straightforward, powerful and data-efficient. Specifically, we first perform attributed RWs on the graph and design an automated program to compose roughly meaningful textual sequences directly from the attributed RWs; then we fine-tune an LM using the RW-based textual sequences and extract embedding vectors from the LM, which encapsulates both attribute semantics and graph structures. In our experiments, we evaluate the learned node embeddings towards different downstream prediction tasks on multiple real-world attributed graph datasets and observe significant improvements over a comprehensive set of state-of-the-art unsupervised node embedding methods. We believe this work opens a door for more sophisticated technical designs and empirical evaluations toward the leverage of LMs for the modeling of real-world graphs.</p>","PeriodicalId":72099,"journal":{"name":"Advances in neural information processing systems","volume":"36 ","pages":"13308-13325"},"PeriodicalIF":0.0,"publicationDate":"2023-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11315369/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141918219","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Jacob Granley, Tristan Fauvel, Matthew Chalk, Michael Beyeler
{"title":"Human-in-the-Loop Optimization for Deep Stimulus Encoding in Visual Prostheses.","authors":"Jacob Granley, Tristan Fauvel, Matthew Chalk, Michael Beyeler","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>Neuroprostheses show potential in restoring lost sensory function and enhancing human capabilities, but the sensations produced by current devices often seem unnatural or distorted. Exact placement of implants and differences in individual perception lead to significant variations in stimulus response, making personalized stimulus optimization a key challenge. Bayesian optimization could be used to optimize patient-specific stimulation parameters with limited noisy observations, but is not feasible for high-dimensional stimuli. Alternatively, deep learning models can optimize stimulus encoding strategies, but typically assume perfect knowledge of patient-specific variations. Here we propose a novel, practically feasible approach that overcomes both of these fundamental limitations. First, a deep encoder network is trained to produce optimal stimuli for any individual patient by inverting a forward model mapping electrical stimuli to visual percepts. Second, a preferential Bayesian optimization strategy utilizes this encoder to optimize patient-specific parameters for a new patient, using a minimal number of pairwise comparisons between candidate stimuli. We demonstrate the viability of this approach on a novel, state-of-the-art visual prosthesis model. We show that our approach quickly learns a personalized stimulus encoder, leads to dramatic improvements in the quality of restored vision, and is robust to noisy patient feedback and misspecifications in the underlying forward model. Overall, our results suggest that combining the strengths of deep learning and Bayesian optimization could significantly improve the perceptual experience of patients fitted with visual prostheses and may prove a viable solution for a range of neuroprosthetic technologies.</p>","PeriodicalId":72099,"journal":{"name":"Advances in neural information processing systems","volume":"36 ","pages":"79376-79398"},"PeriodicalIF":0.0,"publicationDate":"2023-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11232484/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141565279","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Yinghao Aaron Li, Cong Han, Vinay S Raghavan, Gavin Mischler, Nima Mesgarani
{"title":"StyleTTS 2: Towards Human-Level Text-to-Speech through Style Diffusion and Adversarial Training with Large Speech Language Models.","authors":"Yinghao Aaron Li, Cong Han, Vinay S Raghavan, Gavin Mischler, Nima Mesgarani","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>In this paper, we present StyleTTS 2, a text-to-speech (TTS) model that leverages style diffusion and adversarial training with large speech language models (SLMs) to achieve human-level TTS synthesis. StyleTTS 2 differs from its predecessor by modeling styles as a latent random variable through diffusion models to generate the most suitable style for the text without requiring reference speech, achieving efficient latent diffusion while benefiting from the diverse speech synthesis offered by diffusion models. Furthermore, we employ large pre-trained SLMs, such as WavLM, as discriminators with our novel differentiable duration modeling for end-to-end training, resulting in improved speech naturalness. StyleTTS 2 surpasses human recordings on the single-speaker LJSpeech dataset and matches it on the multispeaker VCTK dataset as judged by native English speakers. Moreover, when trained on the LibriTTS dataset, our model outperforms previous publicly available models for zero-shot speaker adaptation. This work achieves the first human-level TTS on both single and multispeaker datasets, showcasing the potential of style diffusion and adversarial training with large SLMs. The audio demos and source code are available at https://styletts2.github.io/.</p>","PeriodicalId":72099,"journal":{"name":"Advances in neural information processing systems","volume":"36 ","pages":"19594-19621"},"PeriodicalIF":0.0,"publicationDate":"2023-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11759097/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143048545","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Aiwen Xu, Yuchen Hou, Cristopher M Niell, Michael Beyeler
{"title":"Multimodal Deep Learning Model Unveils Behavioral Dynamics of V1 Activity in Freely Moving Mice.","authors":"Aiwen Xu, Yuchen Hou, Cristopher M Niell, Michael Beyeler","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>Despite their immense success as a model of macaque visual cortex, deep convolutional neural networks (CNNs) have struggled to predict activity in visual cortex of the mouse, which is thought to be strongly dependent on the animal's behavioral state. Furthermore, most computational models focus on predicting neural responses to static images presented under head fixation, which are dramatically different from the dynamic, continuous visual stimuli that arise during movement in the real world. Consequently, it is still unknown how natural visual input and different behavioral variables may integrate over time to generate responses in primary visual cortex (V1). To address this, we introduce a multimodal recurrent neural network that integrates gaze-contingent visual input with behavioral and temporal dynamics to explain V1 activity in freely moving mice. We show that the model achieves state-of-the-art predictions of V1 activity during free exploration and demonstrate the importance of each component in an extensive ablation study. Analyzing our model using maximally activating stimuli and saliency maps, we reveal new insights into cortical function, including the prevalence of mixed selectivity for behavioral variables in mouse V1. In summary, our model offers a comprehensive deep-learning framework for exploring the computational principles underlying V1 neurons in freely-moving animals engaged in natural behavior.</p>","PeriodicalId":72099,"journal":{"name":"Advances in neural information processing systems","volume":"36 ","pages":"15341-15357"},"PeriodicalIF":0.0,"publicationDate":"2023-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11242920/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141617753","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Emaad Khwaja, Yun S Song, Aaron Agarunov, Bo Huang
{"title":"CELL-E 2: Translating Proteins to Pictures and Back with a Bidirectional Text-to-Image Transformer.","authors":"Emaad Khwaja, Yun S Song, Aaron Agarunov, Bo Huang","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>We present CELL-E 2, a novel bidirectional transformer that can generate images depicting protein subcellular localization from the amino acid sequences (and <i>vice versa</i>). Protein localization is a challenging problem that requires integrating sequence and image information, which most existing methods ignore. CELL-E 2 extends the work of CELL-E, not only capturing the spatial complexity of protein localization and produce probability estimates of localization atop a nucleus image, but also being able to generate sequences from images, enabling <i>de novo</i> protein design. We train and finetune CELL-E 2 on two large-scale datasets of human proteins. We also demonstrate how to use CELL-E 2 to create hundreds of novel nuclear localization signals (NLS). Results and interactive demos are featured at https://bohuanglab.github.io/CELL-E_2/.</p>","PeriodicalId":72099,"journal":{"name":"Advances in neural information processing systems","volume":"36 ","pages":"4899-4914"},"PeriodicalIF":0.0,"publicationDate":"2023-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11254339/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141636011","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Exploring and Interacting with the Set of Good Sparse Generalized Additive Models.","authors":"Chudi Zhong, Zhi Chen, Jiachang Liu, Margo Seltzer, Cynthia Rudin","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>In real applications, interaction between machine learning models and domain experts is critical; however, the classical machine learning paradigm that usually produces only a single model does not facilitate such interaction. Approximating and exploring the Rashomon set, i.e., the set of all near-optimal models, addresses this practical challenge by providing the user with a searchable space containing a diverse set of models from which domain experts can choose. We present algorithms to efficiently and accurately approximate the Rashomon set of sparse, generalized additive models with ellipsoids for fixed support sets and use these ellipsoids to approximate Rashomon sets for many different support sets. The approximated Rashomon set serves as a cornerstone to solve practical challenges such as (1) studying the variable importance for the model class; (2) finding models under user-specified constraints (monotonicity, direct editing); and (3) investigating sudden changes in the shape functions. Experiments demonstrate the fidelity of the approximated Rashomon set and its effectiveness in solving practical challenges.</p>","PeriodicalId":72099,"journal":{"name":"Advances in neural information processing systems","volume":"36 ","pages":"56673-56699"},"PeriodicalIF":0.0,"publicationDate":"2023-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11018320/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140869598","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Chenyu You, Weicheng Dai, Yifei Min, Fenglin Liu, David A Clifton, S Kevin Zhou, Lawrence Staib, James S Duncan
{"title":"Rethinking Semi-Supervised Medical Image Segmentation: A Variance-Reduction Perspective.","authors":"Chenyu You, Weicheng Dai, Yifei Min, Fenglin Liu, David A Clifton, S Kevin Zhou, Lawrence Staib, James S Duncan","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>For medical image segmentation, contrastive learning is the dominant practice to improve the quality of visual representations by contrasting semantically similar and dissimilar pairs of samples. This is enabled by the observation that without accessing ground truth labels, negative examples with truly dissimilar anatomical features, if sampled, can significantly improve the performance. In reality, however, these samples may come from similar anatomical regions and the models may struggle to distinguish the minority tail-class samples, making the tail classes more prone to misclassification, both of which typically lead to model collapse. In this paper, we propose ARCO, a semi-supervised contrastive learning (CL) framework with stratified group theory for medical image segmentation. In particular, we first propose building ARCO through the concept of variance-reduced estimation and show that certain variance-reduction techniques are particularly beneficial in pixel/voxel-level segmentation tasks with extremely limited labels. Furthermore, we theoretically prove these sampling techniques are universal in variance reduction. Finally, we experimentally validate our approaches on eight benchmarks, <i>i.e</i>., five 2D/3D medical and three semantic segmentation datasets, with different label settings, and our methods consistently outperform state-of-the-art semi-supervised methods. Additionally, we augment the CL frameworks with these sampling techniques and demonstrate significant gains over previous methods. We believe our work is an important step towards semi-supervised medical image segmentation by quantifying the limitation of current self-supervision objectives for accomplishing such challenging safety-critical tasks.</p>","PeriodicalId":72099,"journal":{"name":"Advances in neural information processing systems","volume":"36 ","pages":"9984-10021"},"PeriodicalIF":0.0,"publicationDate":"2023-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11136570/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141176950","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Large language models transition from integrating across position-yoked, exponential windows to structure-yoked, power-law windows.","authors":"David Skrill, Sam V Norman-Haignere","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>Modern language models excel at integrating across long temporal scales needed to encode linguistic meaning and show non-trivial similarities to biological neural systems. Prior work suggests that human brain responses to language exhibit hierarchically organized \"integration windows\" that substantially constrain the overall influence of an input token (e.g., a word) on the neural response. However, little prior work has attempted to use integration windows to characterize computations in large language models (LLMs). We developed a simple word-swap procedure for estimating integration windows from black-box language models that does not depend on access to gradients or knowledge of the model architecture (e.g., attention weights). Using this method, we show that trained LLMs exhibit stereotyped integration windows that are well-fit by a convex combination of an exponential and a power-law function, with a partial transition from exponential to power-law dynamics across network layers. We then introduce a metric for quantifying the extent to which these integration windows vary with structural boundaries (e.g., sentence boundaries), and using this metric, we show that integration windows become increasingly yoked to structure at later network layers. None of these findings were observed in an untrained model, which as expected integrated uniformly across its input. These results suggest that LLMs learn to integrate information in natural language using a stereotyped pattern: integrating across position-yoked, exponential windows at early layers, followed by structure-yoked, power-law windows at later layers. The methods we describe in this paper provide a general-purpose toolkit for understanding temporal integration in language models, facilitating cross-disciplinary research at the intersection of biological and artificial intelligence.</p>","PeriodicalId":72099,"journal":{"name":"Advances in neural information processing systems","volume":"36 ","pages":"638-654"},"PeriodicalIF":0.0,"publicationDate":"2023-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10907028/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140023501","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Jiachang Liu, Sam Rosen, Chudi Zhong, Cynthia Rudin
{"title":"OKRidge: Scalable Optimal k-Sparse Ridge Regression.","authors":"Jiachang Liu, Sam Rosen, Chudi Zhong, Cynthia Rudin","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>We consider an important problem in scientific discovery, namely identifying sparse governing equations for nonlinear dynamical systems. This involves solving sparse ridge regression problems to provable optimality in order to determine which terms drive the underlying dynamics. We propose a fast algorithm, OKRidge, for sparse ridge regression, using a novel lower bound calculation involving, first, a saddle point formulation, and from there, either solving (i) a linear system or (ii) using an ADMM-based approach, where the proximal operators can be efficiently evaluated by solving another linear system and an isotonic regression problem. We also propose a method to warm-start our solver, which leverages a beam search. Experimentally, our methods attain provable optimality with run times that are orders of magnitude faster than those of the existing MIP formulations solved by the commercial solver Gurobi.</p>","PeriodicalId":72099,"journal":{"name":"Advances in neural information processing systems","volume":"36 ","pages":"41076-41258"},"PeriodicalIF":0.0,"publicationDate":"2023-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10950455/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140178027","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Chaofei Fan, Nick Hahn, Foram Kamdar, Donald Avansino, Guy H Wilson, Leigh Hochberg, Krishna V Shenoy, Jaimie M Henderson, Francis R Willett
{"title":"Plug-and-Play Stability for Intracortical Brain-Computer Interfaces: A One-Year Demonstration of Seamless Brain-to-Text Communication.","authors":"Chaofei Fan, Nick Hahn, Foram Kamdar, Donald Avansino, Guy H Wilson, Leigh Hochberg, Krishna V Shenoy, Jaimie M Henderson, Francis R Willett","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>Intracortical brain-computer interfaces (iBCIs) have shown promise for restoring rapid communication to people with neurological disorders such as amyotrophic lateral sclerosis (ALS). However, to maintain high performance over time, iBCIs typically need frequent recalibration to combat changes in the neural recordings that accrue over days. This requires iBCI users to stop using the iBCI and engage in supervised data collection, making the iBCI system hard to use. In this paper, we propose a method that enables self-recalibration of communication iBCIs without interrupting the user. Our method leverages large language models (LMs) to automatically correct errors in iBCI outputs. The self-recalibration process uses these corrected outputs (\"pseudo-labels\") to continually update the iBCI decoder online. Over a period of more than one year (403 days), we evaluated our Continual Online Recalibration with Pseudo-labels (CORP) framework with one clinical trial participant. CORP achieved a stable decoding accuracy of 93.84% in an online handwriting iBCI task, significantly outperforming other baseline methods. Notably, this is the longest-running iBCI stability demonstration involving a human participant. Our results provide the first evidence for long-term stabilization of a plug-and-play, high-performance communication iBCI, addressing a major barrier for the clinical translation of iBCIs.</p>","PeriodicalId":72099,"journal":{"name":"Advances in neural information processing systems","volume":"36 ","pages":"42258-42270"},"PeriodicalIF":0.0,"publicationDate":"2023-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11086983/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140913575","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}