Project lead, main contributor, correspondence to alexandre.rame@isir.upmc.fr. Equal experimental contribution, order determined at random. Further information and resources related to this project can be found on this website.

Neural Information Processing Systems http://nips.cc/

Agentic AI "scientists" now use language models to search the literature, run analyses, and generate hypotheses. We evaluate KOSMOS, an autonomous AI scientist, on three problems in radiation biology using simple random-gene null benchmarks. Hypothesis 1: baseline DNA damage response (DDR) capacity across cell lines predicts the p53 transcriptional response after irradiation (GSE30240). Hypothesis 2: baseline expression of OGT and CDO1 predicts the strength of repressed and induced radiation-response modules in breast cancer cells (GSE59732). Hypothesis 3: a 12-gene expression signature predicts biochemical recurrence-free survival after prostate radiotherapy plus androgen deprivation therapy (GSE116918). The DDR-p53 hypothesis was not supported: DDR score and p53 response were weakly negatively correlated (Spearman rho = -0.40, p = 0.76), indistinguishable from random five-gene scores. OGT showed only a weak association (r = 0.23, p = 0.34), whereas CDO1 was a clear outlier (r = 0.70, empirical p = 0.0039). The 12-gene signature achieved a concordance index of 0.61 (p = 0.017) but a non-unique effect size. Overall, KOSMOS produced one well-supported discovery, one plausible but uncertain result, and one false hypothesis, illustrating that AI scientists can generate useful ideas but require rigorous auditing against appropriate null models.

Discovering the antecedents of individuals' influence in collaborative environments is an important, practical, and challenging problem. In this paper, we study interpersonal influence in small groups of individuals who collectively execute a sequence of intellective tasks. We observe that along an issue sequence with feedback, individuals with higher expertise and social confidence are accorded higher interpersonal influence. We also observe that low-performing individuals tend to underestimate their high-performing teammate's expertise. Based on these observations, we introduce three hypotheses and present empirical and theoretical support for their validity. We report empirical evidence on longstanding theories of transactive memory systems, social comparison, and confidence heuristics on the origins of social influence. We propose a cognitive dynamical model inspired by these theories to describe the process by which individuals adjust interpersonal influences over time. We demonstrate the model's accuracy in predicting individuals' influence and provide analytical results on its asymptotic behavior for the case with identically performing individuals. Lastly, we propose a novel approach using deep neural networks on a pre-trained text embedding model for predicting the influence of individuals. Using message contents, message times, and individual correctness collected during tasks, we are able to accurately predict individuals' self-reported influence over time. Extensive experiments verify the accuracy of the proposed models compared to baselines such as structural balance and reflected appraisal model. While the neural networks model is the most accurate, the dynamical model is the most interpretable for influence prediction.

Understanding the consequences of mutation for molecular fitness and function is a fundamental problem in biology.

Neural Information Processing Systems http://nips.cc/

This paper investigates the asymmetric low-rank matrix completion problem, which can be formulated as an unconstrained non-convex optimization problem with a nonlinear least-squares objective function, and is solved via gradient descent methods. Previous gradient descent approaches typically incorporate regularization terms into the objective function to guarantee convergence. However, numerical experiments and theoretical analysis of the gradient flow both demonstrate that the elimination of regularization terms in gradient descent algorithms does not adversely affect convergence performance. By introducing the leave-one-out technique, we inductively prove that the vanilla gradient descent with spectral initialization achieves a linear convergence rate with high probability. Besides, we demonstrate that the balancing regularization term exhibits a small norm during iterations, which reveals the implicit regularization property of gradient descent. Empirical results show that our algorithm has a lower computational cost while maintaining comparable completion performance compared to other gradient descent algorithms.

Active learning for classification seeks to reduce the cost of labeling samples by finding unlabeled examples about which the current model is least certain and sending them to an annotator/expert to label. Bayesian theory can provide a probabilistic view of deep neural network models by asserting a prior distribution over model parameters and estimating the uncertainties by posterior distribution over these parameters. This paper proposes two novel active learning approaches to label one million malware examples belonging to different unknown modern malware families. The first model is Inception-V4+PCA combined with several support vector machine (SVM) algorithms (UTSVM, PSVM, SVM-GSU, TBSVM). The second model is Vision Transformer based Bayesian Neural Networks ViT-BNN. Our proposed ViT-BNN is a state-of-the-art active learning approach that differs from current methods and can apply to any particular task. The experiments demonstrate that the ViT-BNN is more stable and robust in handling uncertainty.

Model merging has gained increasing attention due to its intriguing property: interpolating the parameters of different task-specific fine-tuned models leads to multi-task abilities. However, despite its empirical success, the underlying mechanisms of model merging remain poorly understood. In this work, we delve into the mechanism behind model merging from a representation perspective. Our analysis reveals that model merging achieves multi-task abilities through two key capabilities: i) distinguishing samples from different tasks, and ii) adapting to the corresponding expert model for each sample. These two capabilities allow the merged model to retain task-specific expertise, enabling efficient multi-task adaptation. Building on these insights, we propose \texttt{SE-Merging}, a self-enhanced model merging framework that leverages these two characteristics to dynamically identify the corresponding task for each sample and then adaptively rescales the merging coefficients to further enhance task-specific expertise in the merged model. Notably, \texttt{SE-Merging} achieves dynamic model merging without additional training. Extensive experiments demonstrate that \texttt{SE-Merging} achieves significant performance improvements while remaining compatible with existing model merging techniques.