Motif finding is an important step for the detection of rare events occurring in a set of DNA or protein sequences. Extraction of information about these rare events can lead to new biological discoveries. Motifs are some important patterns that have numerous applications including the identification of transcription factors and their binding sites, composite regulatory patterns, similarity between families of proteins, etc. Although several flavors of motif searching algorithms have been studied in the literature, we study the version known as $ (l, d) $-motif search or Planted Motif Search (PMS). In PMS, given two integers $ l $, $ d $ and $ n $ input sequences we try to find all the patterns of length $ l $ that appear in each of the $ n $ input sequences with at most $ d $ mismatches. We also discuss the quorum version of PMS in our work that finds motifs that are not planted in all the input sequences but at least in $ q $ of the sequences. Our algorithm is mainly based on the algorithms qPMSPrune, qPMS7, TraverStringRef and PMS8. We introduce some techniques to compress the input strings and make faster comparison between strings with bitwise operations. Our algorithm performs a little better than the existing exact algorithms to solve the qPMS problem in DNA sequence. We have also proposed an idea for parallel implementation of our algorithm.
Although adaptive gradient methods have been extensively used in deep learning, their convergence rates proved in the literature are all slower than that of SGD, particularly with respect to their dependence on the dimension. This paper considers the classical RMSProp and its momentum extension and establishes the convergence rate of $\frac{1}{T}\sum_{k=1}^T E\left[\|\nabla f(x^k)\|_1\right]\leq O(\frac{\sqrt{d}C}{T^{1/4}})$ measured by $\ell_1$ norm without the bounded gradient assumption, where $d$ is the dimension of the optimization variable, $T$ is the iteration number, and $C$ is a constant identical to that appeared in the optimal convergence rate of SGD. Our convergence rate matches the lower bound with respect to all the coefficients except the dimension $d$. Since $\|x\|_2\ll\|x\|_1\leq\sqrt{d}\|x\|_2$ for problems with extremely large $d$, our convergence rate can be considered to be analogous to the $\frac{1}{T}\sum_{k=1}^T E\left[\|\nabla f(x^k)\|_2\right]\leq O(\frac{C}{T^{1/4}})$ rate of SGD in the ideal case of $\|\nabla f(x)\|_1=\varTheta(\sqrt{d}\|\nabla f(x)\|_2)$.
The Jump$_k$ benchmark was the first problem for which crossover was proven to give a speedup over mutation-only evolutionary algorithms. Jansen and Wegener (2002) proved an upper bound of $O({\rm poly}(n) + 4^k/p_c)$ for the ($\mu$+1)~Genetic Algorithm ($(\mu+1)$ GA), but only for unrealistically small crossover probabilities $p_c$. To this date, it remains an open problem to prove similar upper bounds for realistic~$p_c$; the best known runtime bound for $p_c = \Omega(1)$ is $O((n/\chi)^{k-1})$, $\chi$ a positive constant. Using recently developed techniques, we analyse the evolution of the population diversity, measured as sum of pairwise Hamming distances, for a variant of the \muga on Jump$_k$. We show that population diversity converges to an equilibrium of near-perfect diversity. This yields an improved and tight time bound of $O(\mu n \log(k) + 4^k/p_c)$ for a range of~$k$ under the mild assumptions $p_c = O(1/k)$ and $\mu \in \Omega(kn)$. For all constant~$k$ the restriction is satisfied for some $p_c = \Omega(1)$. Our work partially solves a problem that has been open for more than 20 years.
Adam with decoupled weight decay, also known as AdamW, is widely acclaimed for its superior performance in language modeling tasks, surpassing Adam with $\ell_2$ regularization in terms of generalization and optimization. However, this advantage is not theoretically well-understood. One challenge here is that though intuitively Adam with $\ell_2$ regularization optimizes the $\ell_2$ regularized loss, it is not clear if AdamW optimizes a specific objective. In this work, we make progress toward understanding the benefit of AdamW by showing that it implicitly performs constrained optimization. More concretely, we show in the full-batch setting, if AdamW converges with any non-increasing learning rate schedule whose partial sum diverges, it must converge to a KKT point of the original loss under the constraint that the $\ell_\infty$ norm of the parameter is bounded by the inverse of the weight decay factor. This result is built on the observation that Adam can be viewed as a smoothed version of SignGD, which is the normalized steepest descent with respect to $\ell_\infty$ norm, and a surprising connection between normalized steepest descent with weight decay and Frank-Wolfe.
The Quantified Constraint Satisfaction Problem is the problem of evaluating a sentence with both quantifiers, over relations from some constraint language, with conjunction as the only connective. We show that for any constraint language on a finite domain the Quantified Constraint Satisfaction Problem is either in $\Pi_{2}^{P}$, or PSpace-complete. Additionally, we build a constraint language on a 6-element domain such that the Quantified Constraint Satisfaction Problem over this language is $\Pi_{2}^{P}$-complete.
Inferring causal structure from data is a challenging task of fundamental importance in science. Observational data are often insufficient to identify a system's causal structure uniquely. While conducting interventions (i.e., experiments) can improve the identifiability, such samples are usually challenging and expensive to obtain. Hence, experimental design approaches for causal discovery aim to minimize the number of interventions by estimating the most informative intervention target. In this work, we propose a novel Gradient-based Intervention Targeting method, abbreviated GIT, that 'trusts' the gradient estimator of a gradient-based causal discovery framework to provide signals for the intervention acquisition function. We provide extensive experiments in simulated and real-world datasets and demonstrate that GIT performs on par with competitive baselines, surpassing them in the low-data regime.
The coalgebraic $\mu$-calculus provides a generic semantic framework for fixpoint logics over systems whose branching type goes beyond the standard relational setup, e.g. probabilistic, weighted, or game-based. Previous work on the coalgebraic $\mu$-calculus includes an exponential-time upper bound on satisfiability checking, which however relies on the availability of tableau rules for the next-step modalities that are sufficiently well-behaved in a formally defined sense; in particular, rule matches need to be representable by polynomial-sized codes, and the sequent duals of the rules need to absorb cut. While such rule sets have been identified for some important cases, they are not known to exist in all cases of interest, in particular ones involving either integer weights as in the graded $\mu$-calculus, or real-valued weights in combination with non-linear arithmetic. In the present work, we prove the same upper complexity bound under more general assumptions, specifically regarding the complexity of the (much simpler) satisfiability problem for the underlying one-step logic, roughly described as the nesting-free next-step fragment of the logic. The bound is realized by a generic global caching algorithm that supports on-the-fly satisfiability checking. Notably, our approach directly accommodates unguarded formulae, and thus avoids use of the guardedness transformation. Example applications include new exponential-time upper bounds for satisfiability checking in an extension of the graded $\mu$-calculus with polynomial inequalities (including positive Presburger arithmetic), as well as an extension of the (two-valued) probabilistic $\mu$-calculus with polynomial inequalities.
Document-level event argument extraction is a crucial yet challenging task within the field of information extraction. Current mainstream approaches primarily focus on the information interaction between event triggers and their arguments, facing two limitations: insufficient context interaction and the ignorance of event correlations. Here, we introduce a novel framework named CARLG (Contextual Aggregation of clues and Role-based Latent Guidance), comprising two innovative components: the Contextual Clues Aggregation (CCA) and the Role-based Latent Information Guidance (RLIG). The CCA module leverages the attention weights derived from a pre-trained encoder to adaptively assimilates broader contextual information, while the RLIG module aims to capture the semantic correlations among event roles. We then instantiate the CARLG framework into two variants based on two types of current mainstream EAE approaches. Notably, our CARLG framework introduces less than 1% new parameters yet significantly improving the performance. Comprehensive experiments across the RAMS, WikiEvents, and MLEE datasets confirm the superiority of CARLG, showing significant superiority in terms of both performance and inference speed compared to major benchmarks. Further analyses demonstrate the effectiveness of the proposed modules.
We propose a polynomially bounded, in time and space, method to decide whether a given 3-SAT formula is satisfiable or not. The tools we use here are, in fact, very simple. We first decide satisfiability for a particular 3-SAT formula, called pivoted 3-SAT and, after a plain transformation, still keeping the polynomial boundaries, it is shown that 3-SAT formulas can be written as pivoted formulas.
In Model Predictive Control (MPC), discrepancies between the actual system and the predictive model can lead to substantial tracking errors and significantly degrade performance and reliability. While such discrepancies can be alleviated with more complex models, this often complicates controller design and implementation. By leveraging the fact that many trajectories of interest are periodic, we show that perfect tracking is possible when incorporating a simple observer that estimates and compensates for periodic disturbances. We present the design of the observer and the accompanying tracking MPC scheme, proving that their combination achieves zero tracking error asymptotically, regardless of the complexity of the unmodelled dynamics. We validate the effectiveness of our method, demonstrating asymptotically perfect tracking on a high-dimensional soft robot with nearly 10,000 states and a fivefold reduction in tracking errors compared to a baseline MPC on small-scale autonomous race car experiments.
Recent artificial intelligence (AI) systems have reached milestones in "grand challenges" ranging from Go to protein-folding. The capability to retrieve medical knowledge, reason over it, and answer medical questions comparably to physicians has long been viewed as one such grand challenge. Large language models (LLMs) have catalyzed significant progress in medical question answering; Med-PaLM was the first model to exceed a "passing" score in US Medical Licensing Examination (USMLE) style questions with a score of 67.2% on the MedQA dataset. However, this and other prior work suggested significant room for improvement, especially when models' answers were compared to clinicians' answers. Here we present Med-PaLM 2, which bridges these gaps by leveraging a combination of base LLM improvements (PaLM 2), medical domain finetuning, and prompting strategies including a novel ensemble refinement approach. Med-PaLM 2 scored up to 86.5% on the MedQA dataset, improving upon Med-PaLM by over 19% and setting a new state-of-the-art. We also observed performance approaching or exceeding state-of-the-art across MedMCQA, PubMedQA, and MMLU clinical topics datasets. We performed detailed human evaluations on long-form questions along multiple axes relevant to clinical applications. In pairwise comparative ranking of 1066 consumer medical questions, physicians preferred Med-PaLM 2 answers to those produced by physicians on eight of nine axes pertaining to clinical utility (p < 0.001). We also observed significant improvements compared to Med-PaLM on every evaluation axis (p < 0.001) on newly introduced datasets of 240 long-form "adversarial" questions to probe LLM limitations. While further studies are necessary to validate the efficacy of these models in real-world settings, these results highlight rapid progress towards physician-level performance in medical question answering.