Daily Papers

Extended-connectivity fingerprints (ECFPs) are a ubiquitous tool in current cheminformatics and molecular machine learning, and one of the most prevalent molecular feature extraction techniques used for chemical prediction. Atom features learned by graph neural networks can be aggregated to compound-level representations using a large spectrum of graph pooling methods; in contrast, sets of detected ECFP substructures are by default transformed into bit vectors using only a simple hash-based folding procedure. We introduce a general mathematical framework for the vectorisation of structural fingerprints via a formal operation called substructure pooling that encompasses hash-based folding, algorithmic substructure-selection, and a wide variety of other potential techniques. We go on to describe Sort & Slice, an easy-to-implement and bit-collision-free alternative to hash-based folding for the pooling of ECFP substructures. Sort & Slice first sorts ECFP substructures according to their relative prevalence in a given set of training compounds and then slices away all but the L most frequent substructures which are subsequently used to generate a binary fingerprint of desired length, L. We computationally compare the performance of hash-based folding, Sort & Slice, and two advanced supervised substructure-selection schemes (filtering and mutual-information maximisation) for ECFP-based molecular property prediction. Our results indicate that, despite its technical simplicity, Sort & Slice robustly (and at times substantially) outperforms traditional hash-based folding as well as the other investigated methods across prediction tasks, data splitting techniques, machine-learning models and ECFP hyperparameters. We thus recommend that Sort & Slice canonically replace hash-based folding as the default substructure-pooling technique to vectorise ECFPs for supervised molecular machine learning.

This paper discusses about a sorting algorithm which uses the concept of buckets where each bucket represents a certain number of digits. A two dimensional data structure is used where one dimension represents buckets i. e; number of digits and each bucket's corresponding dimensions represents the input numbers that belong to that bucket. Each bucket is then individually sorted. Since every preceding bucket elements will always be smaller than the succeeding buckets no comparison between them is required. By doing this we can significantly reduced the time complexity of any sorting algorithm used to sort the given set of inputs.

The Sliced-Wasserstein distance (SW) is a computationally efficient and theoretically grounded alternative to the Wasserstein distance. Yet, the literature on its statistical properties -- or, more accurately, its generalization properties -- with respect to the distribution of slices, beyond the uniform measure, is scarce. To bring new contributions to this line of research, we leverage the PAC-Bayesian theory and a central observation that SW may be interpreted as an average risk, the quantity PAC-Bayesian bounds have been designed to characterize. We provide three types of results: i) PAC-Bayesian generalization bounds that hold on what we refer as adaptive Sliced-Wasserstein distances, i.e. SW defined with respect to arbitrary distributions of slices (among which data-dependent distributions), ii) a principled procedure to learn the distribution of slices that yields maximally discriminative SW, by optimizing our theoretical bounds, and iii) empirical illustrations of our theoretical findings.

Current LLM benchmarks focus on evaluating models' memory of facts and semantic relations, primarily assessing semantic aspects of long-term memory. However, in humans, long-term memory also includes episodic memory, which links memories to their contexts, such as the time and place they occurred. The ability to contextualize memories is crucial for many cognitive tasks and everyday functions. This form of memory has not been evaluated in LLMs with existing benchmarks. To address the gap in evaluating memory in LLMs, we introduce Sequence Order Recall Tasks (SORT), which we adapt from tasks used to study episodic memory in cognitive psychology. SORT requires LLMs to recall the correct order of text segments, and provides a general framework that is both easily extendable and does not require any additional annotations. We present an initial evaluation dataset, Book-SORT, comprising 36k pairs of segments extracted from 9 books recently added to the public domain. Based on a human experiment with 155 participants, we show that humans can recall sequence order based on long-term memory of a book. We find that models can perform the task with high accuracy when relevant text is given in-context during the SORT evaluation. However, when presented with the book text only during training, LLMs' performance on SORT falls short. By allowing to evaluate more aspects of memory, we believe that SORT will aid in the emerging development of memory-augmented models.

Retrieve-and-rerank is a popular retrieval pipeline because of its ability to make slow but effective rerankers efficient enough at query time by reducing the number of comparisons. Recent works in neural rerankers take advantage of large language models for their capability in reasoning between queries and passages and have achieved state-of-the-art retrieval effectiveness. However, such rerankers are resource-intensive, even after heavy optimization. In this work, we introduce Rank-K, a listwise passage reranking model that leverages the reasoning capability of the reasoning language model at query time that provides test time scalability to serve hard queries. We show that Rank-K improves retrieval effectiveness by 23\% over the RankZephyr, the state-of-the-art listwise reranker, when reranking a BM25 initial ranked list and 19\% when reranking strong retrieval results by SPLADE-v3. Since Rank-K is inherently a multilingual model, we found that it ranks passages based on queries in different languages as effectively as it does in monolingual retrieval.

We propose ListT5, a novel reranking approach based on Fusion-in-Decoder (FiD) that handles multiple candidate passages at both train and inference time. We also introduce an efficient inference framework for listwise ranking based on m-ary tournament sort with output caching. We evaluate and compare our model on the BEIR benchmark for zero-shot retrieval task, demonstrating that ListT5 (1) outperforms the state-of-the-art RankT5 baseline with a notable +1.3 gain in the average NDCG@10 score, (2) has an efficiency comparable to pointwise ranking models and surpasses the efficiency of previous listwise ranking models, and (3) overcomes the lost-in-the-middle problem of previous listwise rerankers. Our code, model checkpoints, and the evaluation framework are fully open-sourced at https://github.com/soyoung97/ListT5.

Sorting is a fundamental operation of all computer systems, having been a long-standing significant research topic. Beyond the problem formulation of traditional sorting algorithms, we consider sorting problems for more abstract yet expressive inputs, e.g., multi-digit images and image fragments, through a neural sorting network. To learn a mapping from a high-dimensional input to an ordinal variable, the differentiability of sorting networks needs to be guaranteed. In this paper we define a softening error by a differentiable swap function, and develop an error-free swap function that holds a non-decreasing condition and differentiability. Furthermore, a permutation-equivariant Transformer network with multi-head attention is adopted to capture dependency between given inputs and also leverage its model capacity with self-attention. Experiments on diverse sorting benchmarks show that our methods perform better than or comparable to baseline methods.

We study the conditions under which the convex relaxation of a mixed-integer linear programming formulation for ordered optimization problems, where sorting is part of the decision process, yields integral optimal solutions. Thereby solving the problem exactly in polynomial time. Our analysis identifies structural properties of the input data that influence the integrality of the relaxation. We show that incorporating ordered components introduces additional layers of combinatorial complexity that invalidate the exactness observed in classical (non-ordered) settings. In particular, for certain ordered problems such as the min--max case, the linear relaxation never recovers the integral solution. These results clarify the intrinsic hardness introduced by sorting and reveal that the strength of the relaxation depends critically on the ``proximity'' of the ordered problem to its classical counterpart: problems closer to the non-ordered case tend to admit tighter relaxations, while those further away exhibit substantially weaker behavior. Computational experiments on benchmark instances confirm the predictive value of the integrality conditions and demonstrate the practical implications of exact relaxations for ordered location problems.

Polar slice sampling (Roberts & Rosenthal, 2002) is a Markov chain approach for approximate sampling of distributions that is difficult, if not impossible, to implement efficiently, but behaves provably well with respect to the dimension. By updating the directional and radial components of chain iterates separately, we obtain a family of samplers that mimic polar slice sampling, and yet can be implemented efficiently. Numerical experiments in a variety of settings indicate that our proposed algorithm outperforms the two most closely related approaches, elliptical slice sampling (Murray et al., 2010) and hit-and-run uniform slice sampling (MacKay, 2003). We prove the well-definedness and convergence of our methods under suitable assumptions on the target distribution.

Ranking passages by prompting a large language model (LLM) can achieve promising performance in modern information retrieval (IR) systems. A common approach is to sort the ranking list by prompting LLMs for pairwise comparison. However, sorting-based methods require consistent comparisons to correctly sort the passages, which we show that LLMs often violate. We identify two kinds of intrinsic inconsistency in LLM-based pairwise comparisons: order inconsistency which leads to conflicting results when switching the passage order, and transitive inconsistency which leads to non-transitive triads among all preference pairs. In this paper, we propose LLM-RankFusion, an LLM-based ranking framework that mitigates these inconsistencies and produces a robust ranking list. LLM-RankFusion mitigates order inconsistency using in-context learning (ICL) to demonstrate order-agnostic comparisons and calibration to estimate the underlying preference probability between two passages. We then address transitive inconsistency by aggregating the ranking results from multiple rankers. In our experiments, we empirically show that LLM-RankFusion can significantly reduce inconsistent pairwise comparison results, and improve the ranking quality by making the final ranking list more robust.