51,020 research outputs found
Toward a multilevel representation of protein molecules: comparative approaches to the aggregation/folding propensity problem
This paper builds upon the fundamental work of Niwa et al. [34], which
provides the unique possibility to analyze the relative aggregation/folding
propensity of the elements of the entire Escherichia coli (E. coli) proteome in
a cell-free standardized microenvironment. The hardness of the problem comes
from the superposition between the driving forces of intra- and inter-molecule
interactions and it is mirrored by the evidences of shift from folding to
aggregation phenotypes by single-point mutations [10]. Here we apply several
state-of-the-art classification methods coming from the field of structural
pattern recognition, with the aim to compare different representations of the
same proteins gathered from the Niwa et al. data base; such representations
include sequences and labeled (contact) graphs enriched with chemico-physical
attributes. By this comparison, we are able to identify also some interesting
general properties of proteins. Notably, (i) we suggest a threshold around 250
residues discriminating "easily foldable" from "hardly foldable" molecules
consistent with other independent experiments, and (ii) we highlight the
relevance of contact graph spectra for folding behavior discrimination and
characterization of the E. coli solubility data. The soundness of the
experimental results presented in this paper is proved by the statistically
relevant relationships discovered among the chemico-physical description of
proteins and the developed cost matrix of substitution used in the various
discrimination systems.Comment: 17 pages, 3 figures, 46 reference
On Cognitive Preferences and the Plausibility of Rule-based Models
It is conventional wisdom in machine learning and data mining that logical
models such as rule sets are more interpretable than other models, and that
among such rule-based models, simpler models are more interpretable than more
complex ones. In this position paper, we question this latter assumption by
focusing on one particular aspect of interpretability, namely the plausibility
of models. Roughly speaking, we equate the plausibility of a model with the
likeliness that a user accepts it as an explanation for a prediction. In
particular, we argue that, all other things being equal, longer explanations
may be more convincing than shorter ones, and that the predominant bias for
shorter models, which is typically necessary for learning powerful
discriminative models, may not be suitable when it comes to user acceptance of
the learned models. To that end, we first recapitulate evidence for and against
this postulate, and then report the results of an evaluation in a
crowd-sourcing study based on about 3.000 judgments. The results do not reveal
a strong preference for simple rules, whereas we can observe a weak preference
for longer rules in some domains. We then relate these results to well-known
cognitive biases such as the conjunction fallacy, the representative heuristic,
or the recogition heuristic, and investigate their relation to rule length and
plausibility.Comment: V4: Another rewrite of section on interpretability to clarify focus
on plausibility and relation to interpretability, comprehensibility, and
justifiabilit
Contextualized property market models vs. Generalized mass appraisals: An innovative approach
The present research takes into account the current and widespread need for rational valuation methodologies, able to correctly interpret the available market data. An innovative automated valuation model has been simultaneously implemented to three Italian study samples, each one constituted by two-hundred residential units sold in the years 2016-2017. The ability to generate a "unique" functional form for the three different territorial contexts considered, in which the relationships between the influencing factors and the selling prices are specified by different multiplicative coefficients that appropriately represent the market phenomena of each case study analyzed, is the main contribution of the proposed methodology. The method can provide support for private operators in the assessment of the territorial investment conveniences and for the public entities in the decisional phases regarding future tax and urban planning policies
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